Latest revision as of 13:33, 19 March 2024

Atlases, Images and Videos

Atlas of Drosophila Development, An Atlas following the main events of embryogenesis and post-embryonic development:
Volker Hartenstein and Interactive Fly, Bethesda, MD, USA
FlyBase Maps, A collection of illustrated and electron micrograph maps of polytene chromosomes for the 12 originally sequenced Drosophila species:
FlyBase Maps
FlyMove, an Image, Movie and Interactive Shockwave Resource:
FlyMove, Muenster, Germany
FlyPNS, D. melanogaster embryonic and larval peripheral nervous system:
FlyPNS, UMPC, Paris, France and Columbia University, NY, USA
FlyView, a Drosophila Image Database:
FlyView, Muenster, Germany
GETDB, a Gal4 enhancer trap database:
GETDB, Kyoto Institute of Technology, Kyoto, Japan
Jove, videos of experimental techniques:
Jove, Journal of Visualized Experiments, USA
MidgutAtlas, Gene expression in five pH-defined regions of the larval midgut of D. melanogaster:
Dow laboratory, University of Glascow, Scotland, UK
PeptideAtlas, a multi-organism, publicly accessible compendium of peptides identified in a large set of tandem mass spectrometry proteomics experiments:
Seattle Proteome Center, Seattle, Washington, USA
Virtual Fly Brain - A 3D brain browser with point and click searches for neurons, transgenes and phenotypes:
Virtual Fly Brain, Edinburgh and Cambridge, UK

Cell Lines and Cell Culture

Cellosaurus: A thesaurus of cell lines which attempts to list all cell lines used in biomedical research.
Swiss Institute of Bioinformatics, Geneva, Switzerland
DGRC: Cell Line Catalog:
Drosophila Genomics Resource Center, Indiana University, Bloomington, IN, USA
DGRC: Cell Culture Protocols:
Drosophila Genomics Resource Center, Indiana University, Bloomington, IN, USA
DGRC: Cell Culture FAQ Page:
Drosophila Genomics Resource Center, Indiana University, Bloomington, IN, USA
DGRC: Feeder Cells:
Drosophila Genomics Resource Center, Indiana University, Bloomington, IN, USA
DGRC: Fly Extract:
Drosophila Genomics Resource Center, Indiana University, Bloomington, IN, USA
DRSC: General information about cell lines:
DRSC, Harvard Medical School, Boston, MA, USA
DSRC: Resource information about CRISPR modified cell lines:
DRSC, Harvard Medical School, Boston, MA, USA
DRSC: Protocol information about CRISPR modification of cell lines:
DRSC, Harvard Medical School, Boston, MA, USA

CRISPRs and TALENs

Addgene sgRNA Libraries: Pooled sgRNA libraries for pooled CRISPR cell screening
Addgene, Watertown, MA, USA
CCTop CRISPR/Cas9 optimum target finder:
Center for Organismal Studies, Heidelberg University, Heidelberg, DE
CHOPCHOP CRISPR/Cas9 target online predictor, mammalian and other major model organisms including fly:
University of Bergen, Bergen, Norway
CRISPR-ERA A Fast and Comprehensive Guide RNA Design Tool for Genome Editing, Repression and Activation:
Lei Stanley Qi Lab and Xiaowo Wang Lab, Stanford University, Palo Alto, CA, USA
CRISPR fly design -- reagents, protocols, and results from fly CRISPR/Cas experiments:
Bullolk Lab, MRC Laboratory of Molecular Biology, Cambridge, UK
CRISPResso2 CRISPR Design Tool:
Broad Institute, Cambridge, MA, Harvard Medical School, Boston, MA, Massachusetts General Hospital, Boston, MA, Dana Farber Cancer Center, Boston, MA, Children's Hospital, Boston, MA
CRISPRscan Novel scoring algorithm for selecting sgRNAs
Giraldez Lab, Yale University, New Haven, CT, USA
DGRC Cell lines and vector reagents for CRISPR:
Drosophila Genomics Resource Center (DGRC), Indiana University, Bloomington, IN, USA
DGRC sgRNA libraries:
Drosophila Genomics Resource Center (DGRC), Indiana University, Bloomington, IN, USA
DRSC CRISPR Efficiency Tool for Assessment of Designs:
DRSC/TRiP-FGR, Harvard Medical School, Boston, MA, USA
DRSC Find CRISPRs, Drosophila CRISPR gRNA design search tool:
DRSC/TRiP-FGR, Harvard Medical School, Boston, MA, USA
TRiP CRISPR fly stock information:
DRSC/TRiP-FGR, Harvard Medical School, Boston, MA, USA
DRSC cell-based CRISPR modification:
DRSC/TRiP-FGR, Harvard Medical School, Boston, MA, USA
E-CRISP, Design of CRISPR Constructs:
DKFZ/Boutros lab, Heildelberg, Germany
E-TALEN, Design of TALEN Constructs:
DKFZ/Boutros lab, Heildelberg, Germany
flyCRISPR, Overview:
O'Connor-Giles, Wildonger, and Harrison Labs, University of Wisconsin-Madison, WI, USA
flyCRISPR, Target Finder:
O'Connor-Giles Lab, University of Wisconsin-Madison, WI, USA
Genome Engineering by CRISPR/Cas9 in Drosophila:
NIG/FLY/Ueda lab, Mishima, Japan
Mojo Hand, A TALEN Design Tool:
Ekker lab, Mayo Clinic, Rochester, MN, USA
TALengineering.org, A Comprehensive Resource for Engineered TAL Effector Technology:
Ekker lab, Joung Lab, MGH, Boston, USA
TRiP: Overview of sgRNA vectors:
TRiP, Harvard Medical School, Boston, MA, USA
Zhang Lab CRISPR Plasmids Available from Addgene CRISPR Plasmids:
Zhang Lab, MIT, Boston, MA, USA

Data Repositories

Array Express - Functional Genomics Data:
Array Express, EMBL-EBI, Hinxton, UK
Berkeley Drosophila Genome Project (BDGP):
BDGP, University of California, Berkeley, USA
DDBJ, the DNA Data Bank of Japan:
DDBJ, National Institute of Genetics, Mishima, Japan
EMBL-EBI, The European Bioinformatics Institute:
EMBL-EBI, Hinxton, UK
ENA, European Nucleotide Archive:
ENA, European Nucleotide Archive, EMBL-EBI, Hinxton, UK
ENCODE, Encyclopedia of DNA Elements (including modENCODE and modERN):
ENCODE, Stanford University, Stanford, USA
Gene Disruption Project (GDP):
GDP, Baylor College of Medicine, Texas
Schematic drawings of Transposons
GenBank,the NIH genetic sequence database:
GenBank, NCBI, Bethesda, USA
GEO Datasets, Gene Expression Omnibus:
NCBI, Bethesda, USA
modERN, model organism Encyclopedia of Regulatory Networks:
modERN, University of Washington, Seattle, USA
NCBI, National Center for Biotechnology Information:
Bethesda, MD USA
NCBI Genome Data Viewer, A genome view of Drosophila melanogaster:
NCBI, Bethesda, USA
PubMed, Biomedical literature full-text archive:
PubMed, NCBI, Bethesda, USA
PubMed Central, Biomedical literature citations and abstracts:
PubMed Central, NCBI, Bethesda, USA
SRA, Sequence Read Archive:
SRA, NCBI, Bethesda, MD, USA
UCSC Genome Browser Gateway - D. melanogaster:
UCSC Genome Browser, UC Santa Cruz, Santa Cruz, USA

DNA Reagents

Addgene Highly requested Drosophila plasmids:
Addgene, Watertown, MA, USA
Addgene sgRNA Libraries: Pooled sgRNA libraries for pooled CRISPR cell screening
Addgene, Watertown, MA, USA
DNASU Drosophila plasmids:
DNASU Plasmid Repository, Arizona State University, Tempe, AZ, USA
DGRC DNA Clones Catalog:
Drosophila Genomics Resource Center, Indiana University, Bloomington, IN, USA
DGRC DNA Clone Collections:
Drosophila Genomics Resource Center, Indiana University, Bloomington, IN, USA
DGRC DNA Clone FAQ Page:
Drosophila Genomics Resource Center, Indiana University, Bloomington, IN, USA
DGRC DNA Clone Protocols:
Drosophila Genomics Resource Center, Indiana University, Bloomington, IN, USA
DGRC DNA Vectors Catalog:
Drosophila Genomics Resource Center, Indiana University, Bloomington, IN, USA
DGRC DNA Vectors FAQs Page:
Drosophila Genomics Resource Center, Indiana University, Bloomington, IN, USA
DGRC DNA Vectors Protocols:
Drosophila Genomics Resource Center, Indiana University, Bloomington, IN, USA
TRiP: VALIUM and WALIUM plasmid vector sets:
TRiP, Harvard Medical School, Boston, MA, USA
TRiP: Plasmid cloning protocols:
TRiP, Harvard Medical School, Boston, MA, USA
TRiP: Overview of sgRNA vectors:
TRiP, Harvard Medical School, Boston, MA, USA

Drosophila Genomes Data and Metadata

DrosOmics, a comparative genomics browser to explore omics data in 52 natural populations of D. melanogaster:
Institute of Evolutionary Biology, CSIC, Universitat Pompeu Fabra, Barcelona, Spain
DroSpeGe, a view of Drosophila genome data, with genome maps and BLAST sequence search, for 12 species:
Genome Informatics Lab, Indiana University, Bloomington, Indiana, USA
List of Drosophila reference genome assemblies at FlyBase, NCBI and UCSC. File:DrosophilaGenomeAssemblies.xls (spreadsheet) Updated June 17, 2015
D. albomicans Genome:
D. albomicans Organism Overview, NCBI, USA
D. albomicans Genome Assembly Report, NCBI, USA
D. albomicans Genome Assembly Report, ENA, UK
D. americana Genome:
D. americana Organism Overview, NCBI, USA
D. americana Genome Assembly Report, NCBI, USA
D. americana Genome Assembly Report, ENA, UK
D. ananassae Genome:
D. ananassae Organism Overview, NCBI, USA
D. ananassae Genome Assembly Report, NCBI, USA
D. ananassae Genome Assembly Report, ENA, UK
D. arizonae Genome:
D. arizonae Organism Overview, NCBI, USA
D. arizonae Genome Assembly and Annotation Report, NCBI, USA
D. arizonae Genome Assembly Report, ENA, UK
D. biarmipes Genome:
D. biarmipes Organism Overview, NCBI, USA
D. biarmipes Genome Assembly Report, NCBI, USA
D. biarmipes Genome Assembly Report, ENA, UK
D. bipectinata Genome:
D. bipectinata Organism Overview, NCBI, USA
D. bipectinata Genome Assembly Report, NCBI, USA
D. bipectinata Genome Assembly Report, ENA, UK
D. busckii Genome:
D. busckii Organism Overview, NCBI, USA
D. busckii Genome Assembly Report, NCBI, USA
D. busckii Genome Assembly Report, ENA, UK
D. erecta Genome:
D. erecta Organism Overview, NCBI, USA
D. erecta Genome Assembly Report, NCBI, USA
D. erecta Genome Assembly Report, ENA, UK
D. elegans Genome:
D. elegans Organism Overview, NCBI, USA
D. elegans Genome Assembly Report, NCBI, USA
D. elegans Genome Assembly Report, ENA, UK
D. eugracilis Genome:
D. eugracilis Organism Overview, NCBI, USA
D. eugracilis Genome Assembly Report, NCBI, USA
D. eugracilis Genome Assembly Report, ENA, UK
D. ficusphila Genome:
D. ficusphila Organism Overview, NCBI, USA
D. ficusphila Genome Assembly Report, NCBI, USA
D. ficusphila Genome Assembly Report, ENA, UK
D. grimshawi Genome:
D. grimshawi Organism Overview, NCBI, USA
D. grimshawi Genome Assembly Report, NCBI, USA
D. grimshawi Genome Assembly Report, ENA, UK
D. kikkawai Genome:
D. kikkawai Organism Overview, NCBI, USA
D. kikkawai Genome Assembly Report, NCBI, USA
D. kikkawai Genome Assembly Report, ENA, UK
D. melanogaster Genome:
D. melanogaster Organism Overview, NCBI, USA
D. melanogaster Genome Assembly Report, NCBI, USA
D. melanogaster Genome Assembly Report, ENA, UK
D. miranda Genome:
D. miranda Organism Overview, NCBI, USA
D. miranda Genome Assembly Report, NCBI, USA
D. miranda Genome Assembly Report, ENA, UK
D. mojavensis Genome:
D. mojavensis Organism Overview, NCBI, USA
D. mojavensis Genome Assembly Report, NCBI, USA
D. mojavensis Genome Assembly Report, ENA, UK
D. navojoa Genome:
D. navojoa Organism Overview, NCBI, USA
D. navojoa Genome Assembly Report, NCBI, USA
D. navojoa Genome Assembly Report, ENA, UK
D. persimilis Genome:
D. persimilis Organism Overview, NCBI, USA
D. persimilis Genome Assembly Report, NCBI, USA
D. persimilis Genome Assembly Report, ENA, UK
D. pseudoobscura Genome:
D. pseudoobscura Organism Overview, NCBI, USA
D. pseudoobscura Genome Assembly Report, NCBI, USA
D. pseudoobscura Genome Assembly Report, ENA, UK
D. rhopaloa Genome:
D. rhopaloa Organism Overview, NCBI, USA
D. rhopaloa Genome Assembly Report, NCBI, USA
D. rhopaloa Genome Assembly Report, ENA, UK
D. sechellia Genome:
D. sechellia Organism Overview, NCBI, USA
D. sechellia Genome Assembly Report, NCBI, USA
D. sechellia Genome Assembly Report, ENA, UK
D. simulans Genome:
D. simulans Organism Overview, NCBI, USA
D. simulans Genome Assembly Report, NCBI, USA
D. simulans Genome Assembly Report, ENA, UK
D. suzukii Genome:
D. suzukii Organism Overview, NCBI, USA
D. suzukii Genome Assembly Report, NCBI, USA
D. suzukii Genome Assembly Report, ENA, UK
D. suzukii SpottedWingFlyBase The Spotted Wing Drosophila Project, UC Davis and Oregon State University, USA
D. takahashii Genome:
D. takahashii Organism Overview, NCBI, USA
D. takahashii Genome Assembly Report, NCBI, USA
D. takahashii Genome Assembly Report, ENA, UK
D. virilis Genome:
D. virilis Organism Overview, NCBI, USA
D. virilis Genome Assembly Report, NCBI, USA
D. virilis Genome Assembly Report, ENA, UK
D. willistoni Genome:
D. willistoni Organism Overview, NCBI, USA
D. willistoni Genome Assembly Report, NCBI, USA
D. willistoni Genome Assembly Report, ENA, UK
D. yakuba Genome:
D. yakuba Organism Overview, NCBI, USA
D. yakuba Genome Assembly Report, NCBI, USA
D. yakuba Genome Assembly Report, ENA, UK]

Gene Expression Databases and Tools

BDGP in situ, Patterns of gene expression in Drosophila embryogenesis:
Gene expression database, BDGP, University of California, Berkeley, USA
BGee Normal Gene Expression Data in Animals (based on RNA-Seq, Affymetrix, in situ hybridization, and EST data).
SIB, Swiss Institute of Bioinformatics, University of Lausanne, Lausanne, Switzerland
DIGITtally, Finding Genes of Interest DIGITtally:
DIGITtally, University of Glasgow, Glasgow, UK
FlyAtlas2, for exploring how genes are expressed in the tissues of D. melanogaster:
FlyAtlas2, University of Glasgow, Glasgow, UK
FlyExpress, an Expression Pattern Search Engine:
FlyExpress, Arizona State University, USA
Fly-FISH, A Database of Drosophila Embryo mRNA Localizaton Patterns:
Fly-FISH, University of Toronto, Toronto, Canada
FlyGut-seq, a transcriptomic resource that complements the original Flygut website:
Buchon Lab, Cornell University, Ithaca, NY, USA
FlyLight, Expression Patterns of GAL4, LexA, and Split-GAL4 Driver Lines to enable the visualization and precise manipulation of individual cell types in the Drosophila nervous system:
HHMI, Janelia Farms Research Campus
flytrap, a database of P{GAL4} enhancer traps and their expression in brains:
flytrap, University of Edinburgh, UK
Gene Expression Levels by Cell Line (based on modENCODE data):
DRSC/TRiP-FGR, Harvard Medical School, Boston, MA, USA
GEO Profiles, Gene Expression Omnibus:
GEO, NCBI, Bethesda, MD USA
MidgutAtlas, Gene expression in five pH-defined regions of the larval midgut of D. melanogaster:
Dow laboratory, University of Glascow, Scotland, UK
RNAMiner, A Bioinformatics Protocol for Mining Large RNA-Seq Transcriptomics Data:
Cheng Lab, University of Missouri, Mizzou, Columbia, MO, USA

Gene Groups

FlyBase Gene Groups, Manually curated reports on functionally related genes, based on the literature:
Gene group list, FlyBase
FlyBase Signaling Pathways, Manually curated reports on Signaling Pathways, based on the literature:
Pathways list, FlyBase
GLAD, an Online Database of Gene List Annotations for Drosophila:
DRSC/TRiP-FGR, Harvard Medical School, Boston, MA, USA
Interactive fly, Drosophila genes listed by biochemical function:
Interactive Fly, Thomas Brody and Society for Developmental Biology, MD, USA
Interactive fly, Maternally transcribed genes:
Interactive Fly, Thomas Brody and Society for Developmental Biology, MD, USA
Interactive fly, Zygotically transcribed genes:
Interactive Fly, Thomas Brody and Society for Developmental Biology, MD, USA
KEGG BRITE, Functional hierarchies and binary relationships of biological entities:
KEGG, Kyoto University, Kyoto, Japan and University of Tokyo, Tokyo, Japan
UCSC D. melanogaster Gene Sorter, displays tables of genes related by a variety of characteristics including protein-level homology, similarity of gene expression profiles, and genomic proximity.:
UCSC Genome Informatics Group, University of California, Santa Cruz, Santa Cruz, CA, USA

General Bioinformatics Tools

Addgene, Early Career Researcher Toolbox: Free Online Molecular Biology Tools:
Addgene, Watertown, MA, USA
ApE, A plasmid Editor:
ApE, University of Utah, Salt Lake City, UT, USA
Bioconductor, Open Source Software for Bioinformatics:
Fred Hutchinson Cancer Research Center, Seattle, USA
Bioz, Insights and recommendations for products, equipment and assays:
Palo Alto, CA, USA
Cytoscape -- Network Data Integration, Analysis, and Visualization in a Box:
Cytoscape, Cytoscape Consortium, Canada, France, and USA
FlyMine, an Integrated Database for Drosophila and Anopheles Genomics:
University of Cambridge, United Kingdom
FlyNet, a network prioritization server for Drosophila melanogaster biology:
NetBioLab, Yonsei University, Seoul, Korea

Gene Set Enrichment Analysis

A summary table of selected GSEA tools with information about set up can be found here

DAVID, Database for Annotation, Visualization and Integrated Discovery :
DAVID, Laboratory of Human Retrovirology and Immunoinformatics, Frederick, MD, USA]
Enrichr, Human and Mouse Gene Set Enrichment Analysis:
Enrichr, Center for Bioinfomatics, Mount Sinai, New York, NY, USA
MOET, Multi Ontology Enrichment Tool:
MOET, Rat Genome Database
modEnrichr, Model Organism Gene Set Enrichment Analysis:
modEnrichr, Center for Bioinfomatics, Mount Sinai, New York, NY, USA
flyEnrichr, D.melanogaster Gene Set Enrichment Analysis:
flyEnrichr, Center for Bioinfomatics, Mount Sinai, New York, NY, USA
GO term finder, Generic GO Term Finder:
GOTERMFINDER, Lewis-Sigler Institute for Integrative Genomics, Princeton University, New Jersey, NJ, USA
GOC, GO Enrichment Analysis:
Gene Ontology Consortium
GSEA, Gene Set Enrichment Analysis:
GSEA, Broad Institute, Cambridge, MA, USA
g:Profiler, g:Profiler/g:GOSt:
g:Profiler, Institute of Computer Science, University of Tartu, Tartu, Estonia
GOrilla, Gene Ontology enRIchment anaLysis and visuaLizAtion tool:
GOrilla, Technion, Israel Institute of Technology, Israel
PANGEA, PAthway, Network and Gene-set Enrichment Analysis:
PANGEA, DRSC, Harvard Medical School, Boston, MA, USA
PANTHER, PANTHER GO Enrichment Analysis:
PANTHER, University of Southern California, Los Angeles, CA, USA
REVIGO, Reduce + Visualize Gene Ontology:
REVIGO, Division of electronics, Ruđer Bošković Institute, Zagreb, Croatia
ShinyGO, ShinyGO 0.80:
ShinyGO, South Dakota State University, Brookings, SD, USA
WebGestalt, WebGestalt Gene Set Enrichment Analysis:
WebGestalt, Baylor College of Medicine, Houston, TX, USA

Genome Sequencing Projects

D. pseudoobscura genome project:
D. pseudoobscura Human Genome Sequencing Center, Baylor College of Medicine, USA

Human Disease: Drosophila Models and Orthologous Genes

AGR -- Alliance of Genome Resources:
Alliance of Genome Resources, RGD, MGD, ZFIN, FlyBase, WormBase, SGD, GO consortium, USA and UK
Bloomington Stock Center, Drosophila and Human Disease page:
Bloomington Stock Center, Bloomington, IN, USA
DIOPT-DIST, Disease-related Ortholog Tool:
DRSC-TRiP-FGR, Harvard Medical School, Boston, MA, USA
Drosophila as a Model for Human Diseases:
Interactive Fly, Bethesda, MD, USA
Drosophila Models of Human Disease, a blog by Stephanie Mohr and Annette Parks:
flydiseasemodels.blogspot.com/
FlyNet Human Disease Prioritization:
NetBioLab, Yonsei University, Seoul, Korea
Gene2Function:
Gene2Function, Harvard Medical School, Boston, MA, USA
HuDis, high confidence human disease gene - fly gene ortholog pairs:
DRSC/TRiP-FGR, Harvard Medical School, Boston, MA, USA
MARRVEL, Model organism Aggregated Resources for Rare Variant ExpLoration:
MARRVEL, Baylor College of Medecine, Houston, TX, USA
MORPHIN, Model ORganism Projected on a Human Integrated gene Network:
MORPHIN, Lee Lab, Yonsei University, Korea and Marcotte Lab, University of Texas at Austin, USA.

Interaction and Pathway Databases

BioCyc - FLY -- Curated Drosophila melanogaster Pathways:
FlyCyc, Harvard University, Cambridge, USA
BioGRID, The General Repository for Interaction Datasets:
BioGRID, Mount Sinai Hospital, Toronto, Canada
COMPLEAT, protein COMPLex Enrichment Analysis Tool:
COMPLEAT, DRSC, Harvard Medical School, Boston, MA, USA
DPiM, Drosophila Protein interaction Map:
DPiM, Harvard University Medical School, Boston, MA, USA
DroID, Drosophila Interactions Database:
Drosophila Interaction Database, Detroit, USA
FlyBase Signaling Pathways, Manually curated reports on Signaling Pathways, based on the literature:
Pathways list, FlyBase
FlyNet Gene Prioritization:
NetBioLab, Yonsei University, Seoul, Korea
FlyOde, FLY Organ Developmental Network:
FlyOde, Bogazici University, Istanbul, Turkey
HOMER, Software for motif discovery and next-gen sequencing analysis:
HOMER, University of California at San Diego, San Diego, CA, USA
IM Browser, Drosophila Interactions Database:
IM Browser, Wayne State University, Detroit, MI, USA
IntAct, Molecular Interaction Database:
IntAct, EMBL-EBI, Hinxton, UK
KEGG -- Kyoto Encyclopedia of Genes and Genomes:
KEGG, Kyoto, Japan
MIST -- Molecular Interactions Search Tool:
MIST, Harvard Medical School, Boston, MA, USA
Reactome Pathway Database:
Reactome, OICR, Ontario, Canada, EMBL-EBI, UK, NYU Medical Center, NY, USA
SignaLink, an integrated resource to analyze signaling pathway cross-talks, transcription factors, miRNAs and regulatory enzymes.:
SignaLink, Earlham Institute, Norwich, UK
STRING, Known and Predicted Protein-Protein Interactions
STRING, SIB, Switzerland CPR, Denmark, and EMBL, Heidelberg, Germany
WikiPathways, an open, public platform dedicated to the curation of biological pathways by and for the scientific community:
WikiPathways, Gladstone Institute, San Francisco, CA, USA and Maastricht University, The Netherlands

Metabolomics

FlyMet, A Tissue- and Sex-Specific Metabolomic Atlas and Database :
FlyMet, University of Glasgow, Glasgow, Scotland

Miscellaneous

AGR -- Alliance of Genome Resources:
Alliance of Genome Resources, RGD, MGD, ZFIN, FlyBase, WormBase, SGD, GO consortium, USA and UK
BioLitMine, Biological Literature Mining Tool for Human and Model Organisms:
BioLitMine, Harvard Medical School, Boston, MA, USA
Bionet Archives, a collection of bionet USENET newsgroups and parallel e-mail lists regarding Drosophila:
Genome Informatics Lab, Indiana University, Bloomington, Indiana, USA
Drosophila App, A mobile application developed by Genesee for use in fly research:
Android
Drosophila Information Service:
DIS, Norman, Oklahoma, USA
Drosophila Species Photographs, Photographs of 133 species of Drosophila:
Ehime University, Matsuyama, Japan
Drosophila Workers Unite! A laboratory manual for working with Drosophila:
Michele Markstein Lab, UMass Amherst, Amherst, MA, USA
The Encyclopedia of North American Drosophilids Volume 1: Drosophilids of the Midwest and Northeast:
by T. Werner, Michigan Technological University, Tessa Steenwinkel, Michigan Technological University, and J.Jaenike, University of Rochester
Fly Art - A compendium of arty imagery, sculptures or poetry inspired by Drosophila or flies in the wider sense.:
University of Manchester, Manchester, UK
Fly Labs and References, a large list of fly labs and recent publications:
Interactive Fly, Bethesda, MD, USA
FlyTree, the Drosophila Researcher Genealogy has been incorporated into the Academic Tree Project:
FlyTree, USA
Fully automated drosophila wing landmarking, Automatically finds more than 110 landmark points and creates a digital twin of the drosophila wing:
Datamarkin, Marseille, France
GenAge -- The Ageing Gene Database:
Human Ageing Genomic Resources, Institute of Integrative Biology, Liverpool, UK
Gene Lookup, Gene and Reagent Lookup:
Gene Lookup, DRSC, Harvard Medical School, Boston, MA, USA
GlyCosmos Portal, a Web portal aiming to integrate the glycosciences with the life sciences. It consists of Standards, Repositories and Data Resources, providing information about genes, proteins, lipids, pathways and diseases.:
GlyCosmos, GlyCosmos is a member of the GlySpace Alliance, consisting of ExPASy Glycomics, GlyCosmos, and GlyGen
Interactive Fly, A cyberspace guide to Drosophila development and metazoan evolution
Interactive Fly, Bethesda, MD, USA
Manchester Fly Facility, Resources - A compendium of information on Drosophila melanogaster as a model organism:
University of Manchester, Manchester, UK
Multiplex Fluorescent mRNA In Situ Hybridization, information on how to perform multiplex fluorescent mRNA in situ hybridization on Drosophila embryos:
Bier and McGinnis Labs, UCSD, San Diego, California, USA
What's hot today: Current papers in developmental biology and gene function:
Interactive Fly, Bethesda, MD, USA
The WWW Virtual Library--Drosophila:
Drosophila Virtual Library

Non-coding (ncRNA) Databases and Tools

General

NONCODE, An integrated knowledge database dedicated to ncRNAs, especially lncRNAs:
NONCODE, Tsinghua University and Chinese Academy of Sciences, Beijing, China
Rfam, A collection of RNA sequence families of structural RNAs including non-coding RNA genes as well as cis-regulatory elements :
Rfam, EMBL-EBI, Hinxton, UK
RNAcentral, Integrated access to a comprehensive and up-to-date set of non-coding RNA sequences provided by a collaborating group of Expert Databases :
RNAcentral, EMBL-EBI, Hinxton, UK

lncRNA

LncRBase V.2, a database of information about lncRNAs from 8 species (human, mouse, fly, zebrafish, rat, chicken, C.elegans and cow) :
LncRBase, Bose Institute, West Bengal, India

miRNA

General

miRBase, A searchable database of published miRNA sequences and annotations (current miBase release is 22 - last updated 2018):
miRBase, University of Manchester, UK

NOTE - mirBase Release 21 (June 2014) uses old reference genome assemblies for D. melanogaster (Dmel_Release_5), D. simulans (Dsim_Release_1) and D. pseudoobscura (Dpse_Release_2). Linkouts from D. melanogaster miRNA genes to the Ensembl Genome browser (which displays Dmel_Release_6) will point to the old "Release_5" coordinates, which will be off the mark for many genes, especially those on X, 2R, 3R and 4 chromosomes.

miRNEST, An integrated collection of miRNA predictions from high-throughput sequencing experiments and external database annotations (last updated 2015):
miRNEST, The Adam Mickiewicz University in Poznan, Poznan, Poland
TransmiR, A database of transcription factor-microRNA regulation (last updated 2018):
TransmiR, Peking University Health Science Center, Peking, Chin

miRNA Target Prediction

DIANA microT-CDS, MicroRNA Target Prediction:
DIANA Tools, DIANA LAB, Athens, Greece
MinoTar, Predict microRNA Targets in Coding Sequence (last updated 2010):
MinoTar, DRSC, Harvard Medical School, Boston, MA, USA
TargetScanFly, Prediction of microRNA targets based on miRNA seed region and target conservation (last updated 2012):
TargetScanFly, Whitehead Institute and MIT Dept. of Biology, Cambridge, MA, USA

Validated miRNA Targets

DIANA TarBase, MicroRNA Target Database (last updated 2017):
DIANA TarBase, DIANA LAB, Athens, Greece
miRTex, A text-mining system that extracts miRNA-gene regulation relations and miRNA-target relations from literature (last updated 2017):
miRTex, University of Delaware, Newark, DE, USA

Comparative miRNA Analysis

microRNAviewer, A global view of homologous miRNA genes in many species (last updated 2012):
microRNAviewer, Tel Aviv University, Tel Aviv, Israel

rRNA

SILVA, High quality ribosomal RNA databases (last updated 2020):
SILVA, Max Planck Institute for Marine Microbiology and Jacobs University, Bremen, Germany

tRNA

tRFdb, A relational database of Transfer RNA related Fragments:
tRFdb, Dutta lab, University of Virginia, Charlottesville, VA, USA

snoRNA

snOPY, a snoRNA orthological gene database providing comprehensive information about snoRNAs, snoRNA gene loci and target RNAs.:
snOPY, University of Miyazaki, Japan

SRP RNA

SRPDB, Signal Recognition Particle Database:
SRPDB, University of Texas Health Science Center, San Antonio, USA

Ontology Resources

BioPortal, a biomedical ontologies repository and browser:
BioPortal, The National Center for Biomedical Ontology, USA
Disease Ontology (DO), ontology of disease terms:
Disease Ontology
Gene Ontology Consortium (GO)
Gene Ontology Consortium
GOrilla -- Gene Ontology enRIchment and anaLysis and viuaLizAtion tool:
GOrilla, Israel
OboEdit, browser for OBO ontologies:
OboEdit
The OBO Foundry, an ontology registry:
OboFoundry
Ontobee, an ontologies browser:
Ontobee, He Group, University of Michigan Medical School, Ann Arbor, Michigan, USA
OLS - Ontology Lookup Service, an ontologies browser:
Ontology Lookup Service, EMBL-EBI, Hinxton, UK
Protege, browser for OWL ontologies:
Protege, Stanford Center for Biomedical Informatics Research, Stanford University School of Medicine, USA
QuickGO, a browser for Gene Ontology terms and annotations:
QuickGO, EMBL-EBI, Hinxton, UK

Orthology Predictions

Compara, Ensembl Compara provides cross-species resources and analyses, at both the sequence level and the gene level.
Ensembl, Hinxton, UK
DIOPT, DRSC Integrative Ortholog Prediction Tool
DRSC/TRiP-FGR, Harvard Medical School, Boston, MA, USA
DIOPT-DIST: DIOPT Diseases and Traits, DRSC Disease Gene Query Tool:
DRSC/TRiP-FGR, Harvard Medical School, Boston, MA, USA
EggNOG, A database of orthologous groups and functional annotation:
Computational Biology Group, EMBL, Heidelberg, Germany
Gene2Function:
Gene2Function, Harvard Medical School, Boston, MA, USA
Hieranoid, An orthology inference method using a hierarchical approach. Hieranoid performs pairwise orthology analysis using InParanoid at each node in a guide tree as it progresses from its leaves to the root.
Hieranoid, Stockholm Bioinformatics Centre, Stockholm, Sweden
HieranoiDB, An online database of orthologs inferred by Hieranoid 2 for a representative set of proteomes.
HieranoiDB, Stockholm Bioinformatics Centre, Stockholm, Sweden
Homologene, An automated system for constructing putative homology groups from the complete gene sets of a wide range of eukaryotic species.
NCBI, Bethesda, MD, USA
InParanoiDB 9, Ortholog groups with inparalogs for proteins and protein domains
InParanoiDB 9, Stockholm Bioinformatics Centre, Stockholm, Sweden
Isobase, A Database of Functionally Related Orthologs, which incorporates PPI network data in addition to sequence similarity.
MIT, Cambridge, MA, USA
MARRVEL, Model organism Aggregated Resources for Rare Variant ExpLoration:
MARRVEL, Baylor College of Medecine, Houston, TX, USA
OMA Browser, The OMA (“Orthologous MAtrix”) project is a method and database for the inference of orthologs among complete genomes.
Nucl. Acids Res. 43 (D1): D240-D249. doi: 10.1093/nar/gku1158
OrthoDB, The Hierarchical Catalog of Orthologs
Zdobnov Computational Evolutionary Genomics group, University of Geneva, Geneva, Switzerland
OrthoFinder, A comprehensive platform for comparative genomics that finds orthogroups and orthologs, infers rooted gene trees for all orthogroups and identifies all of the gene duplication events.
University of Oxford, Oxford, UK
OrthoInspector, A software suite for inference of orthologous relationships between protein coding-genes and an online resource to access and query precomputed orthology databases.
ICube Laboratory, Graffenstaden, France
OrthoMCL, Ortholog Groups of Protein Sequences
EuPathDB
PANTHER, PANTHER Classification System
Thomas Lab, University of Southern California, Los Angeles, CA, USA
PhylomeDB, PhylomeDB is a public database for complete catalogs of gene phylogenies (phylomes)
Comparative Genomics Groups at CRB, Barcelona, Spain
Roundup, A large-scale orthology database using the Reciprocal Smallest Distance (RSD) algorithm.
Wall lab, Stanford University, Palo Alto, CA, USA
TreeFam, A database composed of phylogenetic trees inferred from animal genomes. It provides orthology/parology predictions as well the evolutionary history of genes.
EMBL-EBI, Hinxton, UK

Phylogenetic Comparison Tools

DIOPT, DRSC Integrative Ortholog Prediction Tool:
DRSC/TRiP-FGR, Harvard Medical School, Boston, MA, USA
HomoloGene -- automated system fo constructing putative homology groups:
NCBI, Bethesda, MA, USA
InParanoiDB 9, Ortholog groups with inparalogs for proteins and protein domains
InParanoiDB 9, Stockholm Bioinformatics Centre, Stockholm, Sweden
MANTiS, a phylogenetic framework for multi-species genome comparisons:
MANTiS, UniversitÃ© Libre de Bruxelles, Belgium
OrthoDB, the Hierarchical Catalog of Orthologs:
OrthoDB, University of Geneva, Switzerland
Vista Tools -- Whole Genome Comparative Analysis of the D. melanogaster (CAF1) Genome:
Whole Genome Comparative Analysis of the D. melanogaster (CAF1) Genome, LBNL, USA

Population Biology and Polymorphism Resources

BDGP Single Nucleotide Polymorphism (SNP) Project:
Berkeley Drosophila Genome Project, University of California, Berkeley, USA
Drosophila Genetics Reference Panel:
DGRP, Baylor College of Medicine, Houston, TX and NC State University, Raleigh, NC USA
Drosophila Genetics Reference Panel 2:
DGRP2, NC State University, Raleigh, NC and Baylor College of Medicine, Houston, TX, USA
Drosophila Genome Nexus: a population genomic resource that provides D. melanogaster genomes from multiple sources
University of Wisconsin, Madison, WI, USA
DSPR, Drosophila Synthetic Population Resource:
DSPR, University of Kansas and UC Irvine, USA
Global Diversity Lines: a Five Continent Reference Panel of Sequenced Drosophila melanogaster Strains
Global Diversity Lines, Cornell University, Ithaca, NY, USA

Protein Analysis and Modification

AlphaFold Protein Structure Database, AlphaFold DB provides open access to protein structure predictions; An AI system developed by DeepMind that predicts a protein’s 3D structure from its amino acid sequence:
EMBL-EBI, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK
ExPASy, the SIB Bioinformatics Resource Portal which provides access to scientific databases and software tools in different areas of life sciences:
SIB Swiss Institute of Bioinformatics, Genève, Switzerland
GPCRDB, information system for G protein-coupled receptors (GPCRs):
GPCRDB, The GPCRDB (G Protein-Coupled Receptor Data Base) partnership
InterPro protein domain analysis of Drosophila:
InterPro: protein sequence analysis & classification, EBI, UK
iProteinDB Integrated Protein Database of Post Translational Modifications for Drosophila Genes:
iProteinDB, Harvard Medical School, Boston, MA, USA
MEROPS, an information resource for peptidases:
MEROPS, Wellcome Trust Sanger Institute, Hinxton, UK
ModBase, Database of Comparative Protein Structure Models:
ModBase, UCSF, San Francisco, CA, USA
Panther (Protein Analysis THrough Evolutionary Relationships) protein classification system:
Panther Protein Classification System, Applied Biosystems & Celera, USA
PDB, Protein Data Bank:
PDB, The Research Collaboratory for Structural Bioinformatics (RCSB) consortium
PhospoPep, Protein Phosphorylation Database:
Institute for Systems Biology, Seattle, Washington, USA
ProteinProspector, a proteomics tools for mining sequence databases in conjunction with Mass Spectrometry experiments:
UCSF Mass Spectrometry Facility, San Francisco, California, USA
RBPDB, the database of RNA-binding protein specificities:
RBPDB
SMART, Simple Modular Architecture Research Tool:
SMART, Protein Domain Analysis, EMBL, Heidleberg
UniProtKB, a comprehensive catalog of information on proteins:
UniProtKB, The UniProt Consortium

Public Education

About the history of Drosophila research, An extensive collection of media pertaining to the history of fruit fly research:
Manchester Fly Facility, University of Manchester, UK
droso4schools, An online resource for school lessons using the fruit fly Drosophila:
Manchester Fly Facility, University of Manchester, UK
Drosophila & Computer Programming Game, A scratch computer game based on the Drosophila life cycle:
Manchester Fly Facility, University of Manchester, UK
Experiments with Drosophila for Biology Courses, An e-resource book for laboratory experiments at under- and post-graduate levels and for research projects in Biology courses :
Indian Academy of Sciences, India pdf here
FlyMove, an Image, Movie and Interactive Shockwave Resource:
FlyMove, Muenster, Germany
Lay articles, A collection of lay articles about fly research:
Manchester Fly Facility, University of Manchester, UK
Manchester Fly Facility Public Resource Page:
Manchester Fly Facility, University of Manchester, UK

RNAi

DRSC-TRiP-FGR, DRSC/TRiP Functional Genomics Resources:
DRSC-TRiP-FGR, Harvard Medical School, Boston, MA, USA
Search by gene(s) to find hit information for genes and DRSC amplicons in DRSC screens:
DRSC-TRiP-FGR, Harvard Medical School, Boston, MA, USA
FlyRNAi blog, a DRSC resource concerning RNAi, cell-based assays, Drosophila cell culture, high-throughput screening, & fly biology:
flyrnai.blogspot.com
Fosmid rescue analysis tool for identification of fosmids appropriate for cross-species rescue of RNAi:
DRSC-TRiP-FGR, Harvard Medical School, Boston, MA, USA
GenomeRNAi, Heidelberg, a database of RNA interference (RNAi) screens:
GenomeRNAi, DKFZ, Heidelberg, Germany
GESS, off-target RNAi prediction:
DRSC-TRiP-FGR, Harvard Medical School, Boston, MA, USA
Predicted Off-Target Free Sequence Regions:
DRSC-TRiP-FGR, Harvard Medical School, Boston, MA, USA
RNAiCut, Automated Detection of Significant Genes from Functional Genomic Screens:
Berger Lab, MIT, Boston, MA, USA
RSVP, RNAi Stock Validation & Phenotypes:
DRSC-TRiP-FGR, Harvard Medical School, Boston, MA, USA
SnapDragon, RNAi Design:
DRSC-TRiP-FGR, Harvard Medical School, Boston, MA, USA
TRiP, Transgenic RNAi Project:
DRSC-TRiP-FGR, Harvard Medical School, Boston, MA, USA
Tsinghua Fly Center, THFC RNAi Stock Collection for triggering RNAi in soma and germline:
THFC, Tsinghua Fly Center, Beijing, China
UP-TORR Fly, a tool for identifying updated targets of RNAi reagents:
Updated Targets of RNAi Reagents, DRSC-TRiP-FGR, Harvard Medical School, Boston, MA, USA
VDRC, Vienna Drosophila Resource Center:
Genome-wide transgenic Drosophila RNAi libraries, VDRC, Vienna, Austria

Sequence Analysis

DCPD -- Drosophila Core Promoter Database, A list of 205 Drosophila melanogaster core promoters aligned by their empirically determined transcription start site:
Kadonaga Lab, UCSD, San Diego, California, USA
FlyPrimerBank, a comprehensive qPCR primer database for Drosophila:
FlyPrimerBank, DRSC, Harvard Medical School, Boston, MA, USA
FGENESH, Annotation of animal genomes-genes, promoters, functional motifs, protein sub-cellular localization:
Annotation of genomes, Softberry, USA
Gemme, A fast, scalable and simple method to predict mutational landscapes from natural sequences:
Gemme, Sorbonne University, Paris, France
GenePalette, a tool for genome sequence visualization and navigation:
GenePalette, University of California, San Diego, USA
Genie Gene finder for Drosophila: :
Genie, Berkeley Drosophila Genome Project, University of California, Berkeley, USA
HRMA -- High Resolution Melt Analysis:
HRMA, DRSC, Harvard Medical School, Boston, MA, USA
MEME Suite -- Motif-based Sequence Analysis Tools:
MEME, U. of Queensland, U. of Washington, USA, UCSD, SDSC, NBCR, CBRC, and National Center for Research Resources
RepeatMasker:
RepeatMasker Institute for Systems Biology, Seattle, WA, USA
Splice Site Prediction for Drosophila:
Splice Site Prediction, Berkeley Drosophila Genome Project, University of California, Berkeley, USA
Web Apollo, a collaborative genomic annotation editor:
Web Apollo, LBL, Berkeley, USA

Single Cell RNA-seq

ASAP Automated Single-cell Analysis Pipeline:
ASAP, EPFL, Lausanne, Switzerland, Swiss Institute of Bioinformatics, Lausanne, Switzerland

cisTopic Probabilistic modelling of cis-regulatory topics from single cell epigenomics data:
cisTopic, VIB Center for Brain & Disease Research, Leuven, Belgium, Department of Human Genetics, KU Leuven, Leuven, Belgium

DeepCMC A Neural Networks (NN) based approach for identifying genes that contain spatial information:
DeepCMC, Thomas Jefferson University, Philadelphia, PA, USA

Distmap To spatially map single cell RNA sequencing data by using an existing reference database of in situs:
Distmap, BIMSB and MDC, Berlin, Germany

DRscDB DRSC scRNA-seq DataBase:
DRscDB, DRSC, Harvard Medical School, Boston, USA

DVEX Drosophila Virtual Expression eXplorer:
DVEX, BIMSB and MDC, Berlin, Germany

Fly Cell Atlas A consortium of Drosophila researchers interested in single-cell genomics, transcriptomics, and epigenomics:
Fly Cell Atlas, Founders - Stein Aerts, Leuven, Belgium, Bart Deplancke, Lausanne, Switzerland, Robert Zinzen, Berlin, Germany

Lasso.TopX An approach using the Lasso and ranking statistics for identifying genes that contain spatial information:
Lasso.TopX, Thomas Jefferson University, Philadelphia, PA, USA

novoSpaRc Predicts locations of single cells in space by solely using single-cell RNA sequencing data.:
novoSpaRc, Harvard and Broad Institute, Cambridge, MA, USA, Max Delbrück Center, Berlin, Germany

SCEA Single Cell Expression Atlas - Single Cell Gene Expression Across Species:
SCEA, EMBL-EBI, Hinxton, UK, Sanger Institute, Wellcome Genome Campus, Hinxton, UK, Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK

SCENIC Single-Cell Regulatory Network Inference and Clustering
SCENIC, Center for Brain & Disease Research, Leuven, Belgium, KU Leuven, Leuven, Belgium, University of Liege, Liege, Belgium, VIB Center for Cancer Biology, Leuven, Belgium

SCope Fast Visualization Tool for Large-Scale and High Dimensional Single-Cell Data
SCope, VIB KU Leuven, Leuven, Belgium

Seurat An R package designed for QC, analysis, and exploration of single-cell RNA-seq data.:
Seurat, NYU, NY, NY, USA

VSN A Repository of Pipelines for Single-Cell Data Analysis in Nextflow DSL2:
VSN-Pipelines

Taxonomy

FlyPhenomics, phenotypic differences between species of the D. melanogaster subgroup:
FlyPhenomics, Paris, France
TaxoDros Drosophilidae Taxonomic Database:
Drosophilidae Taxonomic Database, Japan
TaxoDros, the database on Taxonomy of Drosophilidae:
TaxoDros, University of Zurich, Switzerland
Taxonomy, NCBI Taxonomy Database:
NCBI, Bethesda, MD USA
Taxonomy of Drosophilidae - JDD - Japan Drosophila Database
Japan Drosophila Database (JDD) on Taxonomy, Japan

Transcription Regulation Databases and Tools

CIS-BP, The online library of transcription factors and their DNA binding motifs:
CIS-BP, Hughes Lab, University of Toronto, Toronto, Canada and Weirauch lab, Cincinnati Children's Hospital, Cincinnati, OH, USA
EPD, the Eukaryotic Promoter Database:
EPD, Epalinges s/Lausanne, Switzerland
Fly Factor Survey - Database of Drosophila TF DNA-binding Specificities:
FLy Factor Survey, UMass Medical School, Worcester, MA, USA
FlyReg, DNase I Footprint Database - retired
University of Manchester Bioinformatics Resources, University of Manchester, UK
JASPAR, A database of transcription factor (TF) binding profiles stored as position frequency matrices and TF flexible models for TFs across multiple species.
JASPAR
Neural Network Promoter Prediction for Drosophila:
Neural Network Promoter Prediction, Berkeley Drosophila Genome Project, University of California, Berkeley, CA, USA
OnTheFly, Database of Drosophila Transcription Factors and Transcription Factor Binding Sites
OnTheFly, Columbia University, NY, USA
REDfly, Regulatory Element Database for Drosophila:
REDfly, University at Buffalo, New York, Buffalo, NY, USA
ReMap, a large-scale integrative analysis of DNA-binding experiments for Homo sapiens, Mus musculus, Dropshiphila melanogaster, and Arabadopsis thaliana transcriptional regulators based on manual curation of ChIP-seq, ChIP-exo, DAP-seq from public sources:
ReMap, TAGC Inserm, Marseille, France
FlyTF.org, The Drosophila Transcription Factor Database:
FlyTF.org, MRC Cambridge, UK
scEnhancer, A database of single cell enhancer annotation in human, mouse, and fly:
scEnhancer, Sun Yat-sen University, Shenzhen, China and Johns Hopkins University, Baltimore, MD, USA
TRANSFAC, A database of transcription factors and their binding sites:
TRANSFAC, Braunschweig, Germany
UniPROBE, Universal PBM (protein binding microarray) Resource for Oligonucleotide Binding Evaluation:
UniPROBE, Bulyk lab, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA

Suggest a tool or resource

Please contact Flybase to suggest a tool or resource for the list.

@@ Line 1: / Line 1: @@
-=Comparative Analysises and Genome Databases=
+=Atlases, Images and Videos=
-* <span class="bold">Assembly/Alignment/Annotation of 12 related Drosophila species:</span><br />[http://rana.lbl.gov/drosophila/ Assembly/Alignment/Annotation, LBNL, USA]
+* <b>Atlas of Drosophila Development</b>, An Atlas following the main events of embryogenesis and post-embryonic development:<br />[https://www.sdbonline.org/sites/fly/atlas/00atlas.htm Volker Hartenstein and Interactive Fly, Bethesda, MD, USA]
-* <span class="bold">BDGP Single Nucleotide Polymorphism (SNP) Project:</span><br />[http://www.fruitfly.org/SNP/ Berkeley Drosophila Genome Project, University of California, Berkeley, USA]
+* <b>FlyBase Maps</b>, A collection of illustrated and electron micrograph maps of polytene chromosomes for the 12 originally sequenced Drosophila species:<br />[http://flybase.org/wiki/FlyBase:Maps FlyBase Maps]
-* <span class="bold">Berkeley Drosophila Genome Project (BDGP):</span><br />[http://www.fruitfly.org/ BDGP, University of California, Berkeley, USA]
+* <b>FlyMove</b>, an Image, Movie and Interactive Shockwave Resource:<br />[http://flymove.uni-muenster.de/ FlyMove, Muenster, Germany]
-* <span class="bold">BDTNP, ChIP/chip in vivo DNA binding data:</span><br />[http://bdtnp.lbl.gov/Fly-Net/chipchip.jsp?w=summary Berkeley Drosophila Transcription Network Project, University of California, Berkeley, USA]
+* <b>FlyPNS</b>, ''D. melanogaster'' embryonic and larval peripheral nervous system:<br />[http://www.normalesup.org/~vorgogoz/FlyPNS/page1.html FlyPNS, UMPC, Paris, France and Columbia University, NY, USA]
-* <span class="bold">CluSTr protein sequence similarity analysis of Drosophila:</span><br />[http://www.ebi.ac.uk/integr8/ClustrAnalysisPage.do?orgProteomeID=17 CluSTr proteome analysis, EBI, UK]
+* <b>FlyView</b>, a Drosophila Image Database:<br />[http://flyview.uni-muenster.de/ FlyView, Muenster, Germany]
-* <span class="bold">''D. pseudoobscura'' genome project:</span><br />[http://www.hgsc.bcm.tmc.edu/projects/drosophila/ Human Genome Sequencing Center, Baylor College of Medicine, USA]
+* <b>GETDB</b>, a Gal4 enhancer trap database:<br />[https://kyotofly.kit.jp/stocks/GETDB/getdb.html GETDB, Kyoto Institute of Technology, Kyoto, Japan]
-* <span class="bold">''D. simulans'' genome project:</span><br />[http://genome.wustl.edu/genome.cgi?GENOME=Drosophila simulans White 501 Genome Sequencing Center, Washington University, USA]
+* <b>Jove</b>, videos of experimental techniques:<br />[https://www.jove.com/search? Jove, Journal of Visualized Experiments, USA]
-* <span class="bold">''D. yakuba'' genome project:</span><br />[http://genome.wustl.edu/genome.cgi?GENOME=Drosophila yakuba Genome Sequencing Center, Washington University, USA]
+* <b>MidgutAtlas</b>, Gene expression in five pH-defined regions of the larval midgut of D. melanogaster:<br />[https://flyatlas.gla.ac.uk/MidgutAtlas/index.html Dow laboratory, University of Glascow, Scotland, UK]
-* <span class="bold">''D. melanogaster'' UCSC Genome Browser Gateway:</span><br />[http://genome.ucsc.edu/cgi-bin/hgGateway?org=D. melanogaster&db=0 University of California, Santa Cruz, USA]
+* <b>PeptideAtlas</b>, a multi-organism, publicly accessible compendium of peptides identified in a large set of tandem mass spectrometry proteomics experiments: <br />[https://peptideatlas.org/ Seattle Proteome Center, Seattle, Washington, USA]
-* <span class="bold">DDBJ, the DNA Data Bank of Japan:</span><br />[http://www.ddbj.nig.ac.jp/ DDBJ, National Institute of Genetics, Mishima, Japan]
+* <b>Virtual Fly Brain</b> - A 3D brain browser with point and click searches for neurons, transgenes and phenotypes:<br />[http://www.virtualflybrain.org Virtual Fly Brain, Edinburgh and Cambridge, UK]
-* <span class="bold">DNase I Footprint Database</span><nowiki>: </nowiki><br />[http://www.flyreg.org/ University of Manchester Bioinformatics Resources, University of Manchester, UK]
-* <span class="bold">Drosophila Heterochromatin Genome Project (DHGP):</span><br />[http://dhgp.org/ DHGP, Lawrence Berkeley National Laboratory, USA]
-* <span class="bold">''Drosophila melanogaster'' Exon Database (DEDB):</span><br />[http://proline.bic.nus.edu.sg/dedb/ DEDB, National University of Singapore]
-* <span class="bold">Drosophila Polymorphism Database:</span><br />[http://bioinformatica.uab.es/dpdb/ Drosophila Polymorphism Database, Univ. AutÃ²noma de Barcelona, Spain]
-* <span class="bold">Drosophila Population Genomic Project (DPGP):</span><br />[http://www.dpgp.org/ DPGP, University of California, Davis, USA]
-* <span class="bold">Drosophila simulans and yakuba sequencing projects:</span><br />[http://www.dpgp.org/sim_yak/index.html DPGP, University of California, Davis, USA]
-* <span class="bold">Drosophilidae Taxonomic Database:</span><br />[http://bioinfo.lowtem.hokudai.ac.jp/db/modules/stdb/ Drosophilidae Taxonomic Database, Japan]
-* <span class="bold">Drosophilidae Taxonomy - Collection of Papers:</span><br />[http://www.dgrc.kit.ac.jp/~jdd/class/index.html Japan Drosophila Database (JDD) on Taxonomy, Japan]
-* <span class="bold">DRSC, Drosophila RNAi Screening Center:</span><br />[http://www.flyrnai.org/index.html DRSC, Harvard Medical School, Boston, MA, USA]
-* <span class="bold">EMBL Nucleotide Sequence Database:</span><br />[http://www.ebi.ac.uk/embl/ EMBL Nucleotide Sequence Database, EBI, Cambridge, UK]
-* <span class="bold">EPD, the Eukaryotic Promoter Database:</span><br />[http://www.epd.isb-sib.ch/ EPD, Epalinges s/Lausanne, Switzerland]
-* <span class="bold">euGenes, Genomic Information for Eukaryotic Organisms, including Drosophila:</span><br />[http://iubio.bio.indiana.edu/eugenes/  euGenes, Indiana University, USA]
-* <span class="bold">EvoPrinter, Identification of Evolutionarily Resilient DNA Sequences</span><br />[http://evoprinter.ninds.nih.gov/ NINDS, NIH, Bethesda MD, USA]
-* <span class="bold">FLIGHT, Fly database for the Integration of Genomic and High-Throughput data:</span><br />[http://flight.licr.org/ FLIGHT Database, Ludwig Institute for Cancer Research, London, UK]
-* <span class="bold">FlyAtlas, the Drosophila adult gene expression atlas:</span><br />[http://www.flyatlas.org/ FlyAtlas, University of Glasgow, UK]
-* <span class="bold">FlyMine, an integrated database for Drosophila &amp; Anopheles genomics:</span><br />[http://www.flymine.org/ University of Cambridge, United Kingdom]
-* <span class="bold">FlyPhenomics, phenotypic differences between species of the ''D. melanogaster'' subgroup:</span><br />[http://www.normalesup.org/~vorgogoz/FlyPhenomics/ FlyPhenomics, Paris, France]
-* <span class="bold">FlySNP Project:</span><br />[http://flysnp.imp.univie.ac.at/ FlySNP, Austrian Academy of Sciences, Austria]
-* <span class="bold">GenBank,the NIH genetic sequence database:</span><br />[http://www.ncbi.nlm.nih.gov/Genbank/ GenBank, NCBI, Bethesda, MD USA]
-* <span class="bold">GenomeRNAi, Heidelberg, a database of RNA interference (RNAi) screens in cultured Drosophila cells:</span><br />[http://www.dkfz.de/signaling2/rnai/index.php GenomeRNAi, DKFZ, Heidelberg, Germany]
-* <span class="bold">GEO, NCBI's Gene Expression Omnibus:</span><br />[http://www.ncbi.nlm.nih.gov/geo/ GEO, NCBI, Bethesda, MD USA]
-* <span class="bold">GPCRDB, information system for G protein-coupled receptors (GPCRs):</span><br />[http://www.gpcr.org/7tm/ GPCRDB, The GPCRDB (G Protein-Coupled Receptor Data Base) partnership]
-* <span class="bold">Homophila, Human Disease to Drosophila Gene Database:</span><br />[http://superfly.ucsd.edu/homophila/  Homophila, San Diego, USA]
-* <span class="bold">InParanoid, Eukaryotic Ortholog Groups:</span><br />[http://inparanoid.sbc.su.se/cgi-bin/index.cgi InParanoid, Karolinska Institute, Sweden]
-* <span class="bold">InterPro protein domain analysis of Drosophila:</span><br />[http://www.ebi.ac.uk/integr8/InterproAnalysisPage.do?orgProteomeID=17 InterPro proteome analysis, EBI, UK]
-* <span class="bold">MANTiS a phylogenetic framework for multi-species genome comparisons:</span><br />[http://www.mantisdb.org/MANTiS/Welcome.html MANTiS, UniversitÃ© Libre de Bruxelles, Belgium]
-* <span class="bold">MEROPS, an information resource for peptidases:</span><br />[http://merops.sanger.ac.uk/ MEROPS, The Sanger Institute, Cambridge, UK]
-* <span class="bold">miRBase, microRNA data:</span><br />[http://microrna.sanger.ac.uk/sequences/index.shtml miRBase, The Sanger Institute, Cambridge, UK]
-* <span class="bold">MitoDrome, ''Drosophila melanogaster'' nuclear genes encoding for mitochondrial proteins:</span><br />[http://www2.ba.itb.cnr.it/MitoDrome/ MitoDrome, Bari, Italy]
-* <span class="bold">Mitotic Spindle Assembly Database:</span><br />[http://rnai.ucsf.edu/mitospindlescreen/index.html Genes Required for Mitotic Spindle Assembly in S2 cells, University of California, San Francisco, USA]
-* <span class="bold">NHGRI Drosophila Genome Sequencing Proposals, Status of Sequencing:</span><br />[http://genome.gov/page.cfm?pageID=10002154 National Human Genome Research Institute, Bethesda, MD, USA]
-* <span class="bold">Panther protein classification system:</span><br />[http://panther.appliedbiosystems.com/about.jsp Panther Protein Classification System, Applied Biosystems &amp; Celera, USA]
-* <span class="bold">PDB, Protein Data Bank:</span><br />[http://www.rcsb.org/pdb/home/home.do PDB, The Research Collaboratory for Structural Bioinformatics (RCSB) consortium]
-* <span class="bold">PhospoPep - phosphorylation site data from ''D. melanogaster'' cell lines:</span><br />[http://www.phosphopep.org/ The Aebersold group at the ETH in collaboration with the FGCZ in Switzerland, and the ISB, USA.]
-* <span class="bold">Proteome analysis of Drosophila:</span><br />[http://www.ebi.ac.uk/integr8/ProteomeAnalysisAction.do?orgProteomeID=17 Proteome analysis, EBI, UK]
-* <span class="bold">PubMed, Biomedical literature citations and abstracts:</span><br />[http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed PubMed, NCBI, Bethesda, MD USA]
-* <span class="bold">REDfly, Regulatory Element Database for Drosophila:</span><br />[http://redfly.ccr.buffalo.edu/ REDfly, University at Buffalo, New York, USA]
-* <span class="bold">Rfam, RNA families database of alignments and CMs:</span><br />[http://www.sanger.ac.uk/Software/Rfam/ Rfam, the Sanger Institute, Cambridge, UK and Janelia Farm, Ashburn, VA, USA]
-* <span class="bold">Sebida, Sex Bias Database:</span><br />[http://141.61.102.16:8080/sebida/index.php Sebida, MPI Martinsried, Germany]
-* <span class="bold">TaxoDros, the database on Taxonomy of Drosophilidae:</span><br />[http://taxodros.unizh.ch/ TaxoDros, University of Zurich, Switzerland]
-* <span class="bold">The Drosophila Transcription Factor Database:</span><br />[http://www.flytf.org/ FlyTF.org, MRC Cambridge, UK]
-* <span class="bold">The McGill ''Drosophila melanogaster'' Genome Project:</span><br />[http://www.mcgill.ca/Biology/labs/MDGP/home.html McGill Drosophila Genome Project, Canada]
-* <span class="bold">TRANSFAC, A database of transcription factors and their binding sites:</span><br />[http://www.gene-regulation.com/pub/databases.html#transfac TRANSFAC, Braunschweig, Germany]
-* <span class="bold">TransTerm, a Translational Signal Database:</span><br />[http://uther.otago.ac.nz/Transterm.html TransTerm, Dunedin, New Zealand]
-* <span class="bold">UniProtKB, a comprehensive catalog of information on proteins:</span><br />[http://www.pir.uniprot.org/ UniProtKB, The UniProt Consortium]
-* <span class="bold">Whole genome comparative analysis of ''D. melanogaster'' and ''D. pseudoobscura''<nowiki>:</nowiki></span><br />[http://pipeline.lbl.gov/pseudo/ Whole genome analysis, LBNL, USA]
-=Sequence Traces of Drosophila Genomes=
+=Cell Lines and Cell Culture=
+* <b>Cellosaurus</b>: A thesaurus of cell lines which attempts to list all cell lines used in biomedical research.<br /> [https://www.cellosaurus.org/ Swiss Institute of Bioinformatics, Geneva, Switzerland]
+* <b>DGRC: Cell Line Catalog</b>: <br /> [https://dgrc.bio.indiana.edu/ Drosophila Genomics Resource Center, Indiana University, Bloomington, IN, USA]
+* <b>DGRC: Cell Culture Protocols</b>: <br />[https://dgrc.bio.indiana.edu/Protocols?tab=cells Drosophila Genomics Resource Center, Indiana University,  Bloomington, IN, USA]
+* <b>DGRC: Cell Culture FAQ Page</b>: <br />[https://dgrc.bio.indiana.edu/FAQs?tab=cells Drosophila Genomics Resource Center, Indiana University, Bloomington, IN, USA]
+* <b>DGRC: Feeder Cells</b>: <br />[https://dgrc.bio.indiana.edu/cells/FeederCells Drosophila Genomics Resource Center, Indiana University, Bloomington, IN, USA]
+* <b>DGRC: Fly Extract</b>:<br />[https://dgrc.bio.indiana.edu/cells/FlyExtract Drosophila Genomics Resource Center, Indiana University, Bloomington, IN, USA]
+* <b>DRSC: General information about cell lines</b>: <br />[https://fgr.hms.harvard.edu/drosophila-cultured-cell-lines DRSC, Harvard Medical School, Boston, MA, USA]
+* <b>DSRC: Resource information about CRISPR modified cell lines</b>: <br />[https://fgr.hms.harvard.edu/crispr-modified-cell-lines DRSC, Harvard Medical School, Boston, MA, USA]
+* <b>DRSC: Protocol information about CRISPR modification of cell lines</b>: <br />[https://fgr.hms.harvard.edu/cell-based-crispr DRSC, Harvard Medical School, Boston, MA, USA]
-* <span class="bold">''D. ananassae'' genomic sequence trace archives:</span><br />[http://www.ncbi.nlm.nih.gov/Traces/trace.fcgi?cmd=retrieve&s=search&m=obtain&retrieve.x=40&retrieve.y=13&val=species_code='DROSOPHILA ANANASSAE' NCBI Trace Archives, USA]<br />[ftp://ftp.ensembl.org/pub/traces/drosophila_ananassae Ensembl FTP Trace Repository, EBI, UK]
+=CRISPRs and TALENs=
-* <span class="bold">''D. erecta'' genomic sequence trace archives:</span><br />[http://www.ncbi.nlm.nih.gov/Traces/trace.fcgi?cmd=retrieve&s=search&m=obtain&retrieve.x=40&retrieve.y=13&val=species_code='DROSOPHILA ERECTA' NCBI Trace Archives, USA]<br />[ftp://ftp.ensembl.org/pub/traces/drosophila_erecta Ensembl FTP Trace Repository, EBI, UK]
+* <b>Addgene sgRNA Libraries</b>: Pooled sgRNA libraries for pooled CRISPR cell screening <br />[https://www.addgene.org/search/catalog/pooled-libraries/?q=Drosophila Addgene, Watertown, MA, USA]
-* <span class="bold">''D. grimshawi'' genomic sequence trace archives:</span><br />[http://www.ncbi.nlm.nih.gov/Traces/trace.fcgi?cmd=retrieve&s=search&m=obtain&retrieve.x=40&retrieve.y=13&val=species_code='DROSOPHILA GRIMSHAWI' NCBI Trace Archives, USA]<br />[ftp://ftp.ensembl.org/pub/traces/drosophila_grimshawi Ensembl FTP Trace Repository, EBI, UK]
+* <b>CCTop</b> CRISPR/Cas9 optimum target finder:<br />[https://cctop.cos.uni-heidelberg.de/index.html Center for Organismal Studies, Heidelberg University, Heidelberg, DE]
-* <span class="bold">''D. melanogaster'' genomic sequence trace archives:</span><br />[http://www.ncbi.nlm.nih.gov/Traces/trace.fcgi?cmd=retrieve&s=search&m=obtain&retrieve.x=40&retrieve.y=13&val=species_code='DROSOPHILA MELANOGASTER' NCBI Trace Archives, USA]<br />[ftp://ftp.ensembl.org/pub/traces/drosophila_melanogaster Ensembl FTP Trace Repository, EBI, UK]
+* <b>CHOPCHOP</b> CRISPR/Cas9 target online predictor, mammalian and other major model organisms including fly:<br />[https://chopchop.cbu.uib.no/ University of Bergen, Bergen, Norway]
-* <span class="bold">''D. mojavensis'' genomic sequence trace archives:</span><br />[http://www.ncbi.nlm.nih.gov/Traces/trace.fcgi?cmd=retrieve&s=search&m=obtain&retrieve.x=40&retrieve.y=13&val=species_code='DROSOPHILA MOJAVENSIS' NCBI Trace Archives, USA]<br />[ftp://ftp.ensembl.org/pub/traces/drosophila_mojavensis Ensembl FTP Trace Repository, EBI, UK]
+* <b>CRISPR-ERA</b> A Fast and Comprehensive Guide RNA Design Tool for Genome Editing, Repression and Activation:<br />[http://crispr-era.stanford.edu// Lei Stanley Qi Lab and Xiaowo Wang Lab, Stanford University, Palo Alto, CA, USA]
-* <span class="bold">''D. persimilis'' genomic sequence trace archives:</span><br />[http://www.ncbi.nlm.nih.gov/Traces/trace.fcgi?cmd=retrieve&s=search&m=obtain&retrieve.x=40&retrieve.y=13&val=species_code='DROSOPHILA PERSIMILIS' NCBI Trace Archives, USA]<br />[ftp://ftp.ensembl.org/pub/traces/drosophila_persimilis Ensembl FTP Trace Repository, EBI, UK]
+* <b>CRISPR fly design</b> -- reagents, protocols, and results from fly CRISPR/Cas experiments:<br />[http://crisprflydesign.org/ Bullolk Lab, MRC Laboratory of Molecular Biology, Cambridge, UK]
-* <span class="bold">''D. pseudoobscura'' genomic sequence trace archives:</span><br />[http://www.ncbi.nlm.nih.gov/Traces/trace.fcgi?cmd=retrieve&s=search&m=obtain&retrieve.x=40&retrieve.y=13&val=species_code='DROSOPHILA PSEUDOOBSCURA' NCBI Trace Archives, USA]<br />[ftp://ftp.ensembl.org/pub/traces/drosophila_pseudoobscura Ensembl FTP Trace Repository, EBI, UK]
+* <b>CRISPResso2 </b> CRISPR Design Tool:<br />[http://crispresso.pinellolab.org/submission Broad Institute, Cambridge, MA, Harvard Medical School, Boston, MA, Massachusetts General Hospital, Boston, MA, Dana Farber Cancer Center, Boston, MA, Children's Hospital, Boston, MA]
-* <span class="bold">''D. sechellia'' genomic sequence trace archives:</span><br />[http://www.ncbi.nlm.nih.gov/Traces/trace.fcgi?cmd=retrieve&s=search&m=obtain&retrieve.x=40&retrieve.y=13&val=species_code='DROSOPHILA SECHELLIA' NCBI Trace Archives, USA]<br />[ftp://ftp.ensembl.org/pub/traces/drosophila_sechellia Ensembl FTP Trace Repository, EBI, UK]
+* <b>CRISPRscan</b> Novel scoring algorithm for selecting sgRNAs<br />[http://www.crisprscan.org// Giraldez Lab, Yale University, New Haven, CT, USA]
-* <span class="bold">''D. simulans'' genomic sequence trace archives:</span><br />[http://www.ncbi.nlm.nih.gov/Traces/trace.fcgi?cmd=retrieve&s=search&m=obtain&retrieve.x=40&retrieve.y=13&val=species_code='DROSOPHILA SIMULANS' NCBI Trace Archives, USA]<br />[ftp://ftp.ensembl.org/pub/traces/drosophila_simulans Ensembl FTP Trace Repository, EBI, UK]
+* <b>DGRC Cell lines and vector reagents for CRISPR</b>:<br />[https://dgrc.bio.indiana.edu/Search?category=&query=crispr Drosophila Genomics Resource Center (DGRC), Indiana University, Bloomington, IN, USA]
-* <span class="bold">''D. virilis'' genomic sequence trace archives:</span><br />[http://www.ncbi.nlm.nih.gov/Traces/trace.fcgi?cmd=retrieve&s=search&m=obtain&retrieve.x=40&retrieve.y=13&val=species_code='DROSOPHILA VIRILIS' NCBI Trace Archives, USA]<br />[ftp://ftp.ensembl.org/pub/traces/drosophila_virilis Ensembl FTP Trace Repository, EBI, UK]
+* <b>DGRC sgRNA libraries</b>:<br />[https://dgrc.bio.indiana.edu/gRNA Drosophila Genomics Resource Center (DGRC), Indiana University, Bloomington, IN, USA]
-* <span class="bold">''D. willistoni'' genomic sequence trace archives:</span><br />[http://www.ncbi.nlm.nih.gov/Traces/trace.fcgi?cmd=retrieve&s=search&m=obtain&retrieve.x=40&retrieve.y=13&val=species_code='DROSOPHILA WILLISTONI' NCBI Trace Archives, USA]<br />[ftp://ftp.ensembl.org/pub/traces/drosophila_willistoni Ensembl FTP Trace Repository, EBI, UK]
+* <b>DRSC CRISPR Efficiency Tool for Assessment of Designs</b>:<br />[https://www.flyrnai.org/evaluateCrispr/ DRSC/TRiP-FGR, Harvard Medical School, Boston, MA, USA]
-* <span class="bold">''D. yakuba'' genomic sequence trace archives:</span><br />[http://www.ncbi.nlm.nih.gov/Traces/trace.fcgi?cmd=retrieve&s=search&m=obtain&retrieve.x=40&retrieve.y=13&val=species_code='DROSOPHILA YAKUBA' NCBI Trace Archives, USA]<br />[ftp://ftp.ensembl.org/pub/traces/drosophila_yakuba Ensembl FTP Trace Repository, EBI, UK]
+* <b>DRSC Find CRISPRs</b>, Drosophila CRISPR gRNA design search tool:<br />[https://www.flyrnai.org/crispr2/ DRSC/TRiP-FGR, Harvard Medical School, Boston, MA, USA]
+* <b>TRiP CRISPR fly stock information</b>:<br />[https://fgr.hms.harvard.edu/crispr-fly-stocks-and-vectors DRSC/TRiP-FGR, Harvard Medical School, Boston, MA, USA]
+* <b>DRSC cell-based CRISPR modification</b>:<br />[https://fgr.hms.harvard.edu/publications/technology/fly-cell-based-crispr DRSC/TRiP-FGR, Harvard Medical School, Boston, MA, USA]
+* <b>E-CRISP</b>, Design of CRISPR Constructs:<br />[http://www.e-crisp.org/E-CRISP/designcrispr.html DKFZ/Boutros lab, Heildelberg, Germany]
+* <b>E-TALEN</b>, Design of TALEN Constructs:<br />[http://www.e-talen.org/E-TALEN/ DKFZ/Boutros lab, Heildelberg, Germany]
+* <b>flyCRISPR</b>, Overview: <br />[https://flycrispr.org/ O'Connor-Giles, Wildonger, and Harrison Labs, University of Wisconsin-Madison, WI, USA]
+* <b>flyCRISPR</b>, Target Finder:<br />[https://flycrispr.org/target-finder/ O'Connor-Giles Lab, University of Wisconsin-Madison, WI, USA]
+* <b>Genome Engineering by CRISPR/Cas9 in Drosophila</b>:<br />[https://shigen.nig.ac.jp/fly/nigfly/cas9/ NIG/FLY/Ueda lab, Mishima, Japan]
+* <b>Mojo Hand</b>, A TALEN Design Tool:<br />[http://www.talendesign.org/ Ekker lab, Mayo Clinic, Rochester, MN, USA]
+* <b>TALengineering.org</b>, A Comprehensive Resource for Engineered TAL Effector Technology:<br />[http://talengineering.org/ Ekker lab, Joung Lab, MGH, Boston, USA]
+* <b>TRiP: Overview of sgRNA vectors</b>:<br />[https://fgr.hms.harvard.edu/sgrna-vectors TRiP, Harvard Medical School, Boston, MA, USA]
+* <b>Zhang Lab CRISPR Plasmids Available from Addgene</b> CRISPR Plasmids:<br />[https://www.addgene.org/crispr/zhang/  Zhang Lab, MIT, Boston, MA, USA]
+=Data Repositories=
+* <b>Array Express</b> - Functional Genomics Data:<br />[https://www.ebi.ac.uk/arrayexpress/ Array Express, EMBL-EBI, Hinxton, UK]
+* <b>Berkeley Drosophila Genome Project (BDGP)</b>:<br />[https://www.fruitfly.org/ BDGP, University of California, Berkeley, USA]
+* <b>DDBJ</b>, the DNA Data Bank of Japan:<br />[https://www.ddbj.nig.ac.jp/index-e.html DDBJ, National Institute of Genetics, Mishima, Japan]
+* <b>EMBL-EBI</b>, The European Bioinformatics Institute:<br />[https://www.ebi.ac.uk/ EMBL-EBI, Hinxton, UK]
+* <b>ENA</b>, European Nucleotide Archive:<br />[https://www.ebi.ac.uk/ena/browser/home ENA, European Nucleotide Archive, EMBL-EBI, Hinxton, UK]
+* <b>ENCODE</b>, Encyclopedia of DNA Elements (including modENCODE and modERN):<br />[https://www.encodeproject.org/ ENCODE, Stanford University, Stanford, USA]
+* <b>Gene Disruption Project (GDP)</b>:<br />[https://flypush.research.bcm.edu/pscreen/index.php GDP, Baylor College of Medicine, Texas]<br />[https://flypush.research.bcm.edu/pscreen/transposons.html Schematic drawings of Transposons]
+* <b>GenBank</b>,the NIH genetic sequence database:<br />[https://www.ncbi.nlm.nih.gov/genbank/ GenBank, NCBI, Bethesda, USA]
+* <b>GEO Datasets</b>, Gene Expression Omnibus:<br />[https://www.ncbi.nlm.nih.gov/geo/info/datasets.html NCBI, Bethesda, USA]
+* <b>modERN</b>, model organism Encyclopedia of Regulatory Networks:<br />[http://epic.gs.washington.edu/modERN/ modERN, University of Washington, Seattle, USA]
+* <b>NCBI</b>, National Center for Biotechnology Information:<br />[http://www.ncbi.nlm.nih.gov Bethesda, MD USA]
+* <b>NCBI Genome Data Viewer</b>, A genome view of Drosophila melanogaster:<br />[https://www.ncbi.nlm.nih.gov/genome/gdv/?org=drosophila-melanogaster NCBI, Bethesda, USA]
+* <b>PubMed</b>, Biomedical literature full-text archive:<br />[https://pubmed.ncbi.nlm.nih.gov/ PubMed, NCBI, Bethesda, USA]
+* <b>PubMed Central</b>, Biomedical literature citations and abstracts:<br />[https://www.ncbi.nlm.nih.gov/pmc/ PubMed Central, NCBI, Bethesda, USA]
+* <b>SRA</b>, Sequence Read Archive:<br />[https://www.ncbi.nlm.nih.gov/sra SRA, NCBI, Bethesda, MD, USA]
+* <b>UCSC Genome Browser Gateway</b> - D. melanogaster:<br />[http://genome.ucsc.edu/cgi-bin/hgGateway UCSC Genome Browser, UC Santa Cruz, Santa Cruz, USA]
+=DNA Reagents=
+* <b>Addgene Highly requested Drosophila plasmids</b>: <br />[https://www.addgene.org/search/catalog/pooled-libraries/?q=Drosophila Addgene, Watertown, MA, USA]
+* <b>Addgene sgRNA Libraries</b>: Pooled sgRNA libraries for pooled CRISPR cell screening <br />[https://www.addgene.org/search/catalog/pooled-libraries/?q=Drosophila Addgene, Watertown, MA, USA]
+* <b>DNASU Drosophila plasmids</b>: <br />[https://dnasu.org/DNASU/AdvancedSearchOptions.do?species=Drosophila%20melanogaster&psi=0 DNASU Plasmid Repository, Arizona State University, Tempe, AZ, USA]
+* <b>DGRC DNA Clones Catalog</b>:<br />[https://dgrc.bio.indiana.edu/clones/Catalog Drosophila Genomics Resource Center, Indiana University, Bloomington, IN, USA]
+* <b>DGRC DNA Clone Collections</b>:<br />[https://dgrc.bio.indiana.edu/clones/BulkCollections  Drosophila Genomics Resource Center, Indiana University, Bloomington, IN, USA]
+* <b>DGRC DNA Clone FAQ Page</b>:<br />[https://dgrc.bio.indiana.edu/FAQs?tab=clones Drosophila Genomics Resource Center, Indiana University, Bloomington, IN, USA]
+* <b>DGRC DNA Clone Protocols</b>:<br />[https://dgrc.bio.indiana.edu/Protocols?tab=clones Drosophila Genomics Resource Center, Indiana University, Bloomington, IN, USA]
+* <b>DGRC DNA Vectors Catalog</b>:<br />[https://dgrc.bio.indiana.edu/vectors/Catalog Drosophila Genomics Resource Center, Indiana University, Bloomington, IN, USA]
+* <b>DGRC DNA Vectors FAQs Page</b>:<br />[https://dgrc.bio.indiana.edu/FAQs?tab=vectors Drosophila Genomics Resource Center, Indiana University, Bloomington, IN, USA]
+* <b>DGRC DNA Vectors Protocols</b>:<br />[https://dgrc.bio.indiana.edu/Protocols?tab=vectors Drosophila Genomics Resource Center, Indiana University, Bloomington, IN, USA]
+* <b>TRiP: VALIUM and WALIUM plasmid vector sets</b>:<br />[https://fgr.hms.harvard.edu/trip-plasmid-vector-sets TRiP, Harvard Medical School, Boston, MA, USA]
+* <b>TRiP: Plasmid cloning protocols</b>:<br />[https://fgr.hms.harvard.edu/cloning-and-sequencing TRiP, Harvard Medical School, Boston, MA, USA]
+* <b>TRiP: Overview of sgRNA vectors</b>:<br />[https://fgr.hms.harvard.edu/sgrna-vectors TRiP, Harvard Medical School, Boston, MA, USA]
+=Drosophila Genomes Data and Metadata=
+* <b>DrosOmics</b>, a comparative genomics browser to explore omics data in 52 natural populations of D. melanogaster:<br />[https://www.biologiaevolutiva.org/gonzalez_lab/drosomics/ Institute of Evolutionary Biology, CSIC, Universitat Pompeu Fabra, Barcelona, Spain]
+* <b>DroSpeGe</b>, a view of Drosophila genome data, with genome maps and BLAST sequence search, for 12 species:<br />[http://insects.eugenes.org/species/ Genome Informatics Lab, Indiana University, Bloomington, Indiana, USA]
+* <b>List of Drosophila reference genome assemblies</b> at FlyBase, NCBI and UCSC. [[File:DrosophilaGenomeAssemblies.xls]] (spreadsheet) ''Updated June 17, 2015''
+* <b>''D. albomicans'' Genome</b>:<br />[https://www.ncbi.nlm.nih.gov/genome/2712/ ''D. albomicans'' Organism Overview, NCBI, USA]<br />[https://www.ncbi.nlm.nih.gov/genome/genomes/2712/ ''D. albomicans'' Genome Assembly Report, NCBI, USA]<br />[http://www.ebi.ac.uk/ena/data/view/GCA_000298335 ''D. albomicans'' Genome Assembly Report, ENA, UK]
+* <b>''D. americana'' Genome</b>:<br />[https://www.ncbi.nlm.nih.gov/genome/10917 ''D. americana'' Organism Overview, NCBI, USA]<br />[https://www.ncbi.nlm.nih.gov/genome/genomes/10917 ''D. americana'' Genome Assembly Report, NCBI, USA]<br />[http://www.ebi.ac.uk/ena/data/view/GCA_001245305.1 ''D. americana'' Genome Assembly Report, ENA, UK]
+* <b>''D. ananassae'' Genome</b>:<br />[https://www.ncbi.nlm.nih.gov/genome/244/ ''D. ananassae'' Organism Overview, NCBI, USA]<br />[https://www.ncbi.nlm.nih.gov/genome/genomes/244/ ''D. ananassae'' Genome Assembly Report, NCBI, USA]<br />[http://www.ebi.ac.uk/ena/data/view/GCA_000005115 ''D. ananassae'' Genome Assembly Report, ENA, UK]
+* <b>''D. arizonae'' Genome</b>:<br />[https://www.ncbi.nlm.nih.gov/genome/45090/ ''D. arizonae'' Organism Overview, NCBI, USA]<br />[https://www.ncbi.nlm.nih.gov/genome/genomes/45090/ ''D. arizonae'' Genome Assembly and Annotation Report, NCBI, USA]<br />[https://www.ebi.ac.uk/ena/data/view/GCA_001654025 ''D. arizonae'' Genome Assembly Report, ENA, UK]
+* <b>''D. biarmipes'' Genome</b>:<br />[https://www.ncbi.nlm.nih.gov/genome/3499/ ''D. biarmipes'' Organism Overview, NCBI, USA]<br />[https://www.ncbi.nlm.nih.gov/genome/genomes/3499/ ''D. biarmipes'' Genome Assembly Report, NCBI, USA]<br />[http://www.ebi.ac.uk/ena/data/view/GCA_000233415 ''D. biarmipes'' Genome Assembly Report, ENA, UK]
+* <b>''D. bipectinata'' Genome</b>:<br />[https://www.ncbi.nlm.nih.gov/genome/3489/ ''D. bipectinata'' Organism Overview, NCBI, USA]<br />[https://www.ncbi.nlm.nih.gov/genome/genomes/3489/ ''D. bipectinata'' Genome Assembly Report, NCBI, USA]<br />[http://www.ebi.ac.uk/ena/data/view/GCA_000236285 ''D. bipectinata'' Genome Assembly Report, ENA, UK]
+* <b>''D. busckii'' Genome</b>:<br />[https://www.ncbi.nlm.nih.gov/genome/38276/ ''D. busckii'' Organism Overview, NCBI, USA]<br />[https://www.ncbi.nlm.nih.gov/genome/genomes/38276/ ''D. busckii'' Genome Assembly Report, NCBI, USA]<br />[http://www.ebi.ac.uk/ena/data/view/GCA_001277935 ''D. busckii'' Genome Assembly Report, ENA, UK]
+* <b>''D. erecta'' Genome</b>:<br />[https://www.ncbi.nlm.nih.gov/genome/250/ ''D. erecta'' Organism Overview, NCBI, USA]<br />[https://www.ncbi.nlm.nih.gov/genome/genomes/250/ ''D. erecta'' Genome Assembly Report, NCBI, USA]<br />[http://www.ebi.ac.uk/ena/data/view/GCA_000005135 ''D. erecta'' Genome Assembly Report, ENA, UK]
+* <b>''D. elegans'' Genome</b>:<br />[https://www.ncbi.nlm.nih.gov/genome/3490 ''D. elegans'' Organism Overview, NCBI, USA]<br />[https://www.ncbi.nlm.nih.gov/genome/genomes/3490 ''D. elegans'' Genome Assembly Report, NCBI, USA]<br />[http://www.ebi.ac.uk/ena/data/view/GCA_000224195 ''D. elegans'' Genome Assembly Report, ENA, UK]
+* <b>''D. eugracilis'' Genome</b>:<br />[https://www.ncbi.nlm.nih.gov/genome/6863/ ''D. eugracilis'' Organism Overview, NCBI, USA]<br />[https://www.ncbi.nlm.nih.gov/genome/genomes/6863/ ''D. eugracilis'' Genome Assembly Report, NCBI, USA]<br />[http://www.ebi.ac.uk/ena/data/view/GCA_000236325 ''D. eugracilis'' Genome Assembly Report, ENA, UK]
+* <b>''D. ficusphila'' Genome</b>:<br />[https://www.ncbi.nlm.nih.gov/genome/3491/ ''D. ficusphila'' Organism Overview, NCBI, USA]<br />[https://www.ncbi.nlm.nih.gov/genome/genomes/3491/ ''D. ficusphila'' Genome Assembly Report, NCBI, USA]<br />[http://www.ebi.ac.uk/ena/data/view/GCA_000220665 ''D. ficusphila'' Genome Assembly Report, ENA, UK]
+* <b>''D. grimshawi'' Genome</b>:<br />[https://www.ncbi.nlm.nih.gov/genome/257/ ''D. grimshawi'' Organism Overview, NCBI, USA]<br />[https://www.ncbi.nlm.nih.gov/genome/genomes/257/ ''D. grimshawi'' Genome Assembly Report, NCBI, USA]<br />[http://www.ebi.ac.uk/ena/data/view/GCA_000005155 ''D. grimshawi'' Genome Assembly Report, ENA, UK]
+* <b>''D. kikkawai'' Genome</b>:<br />[https://www.ncbi.nlm.nih.gov/genome/3492/ ''D. kikkawai'' Organism Overview, NCBI, USA]<br />[https://www.ncbi.nlm.nih.gov/genome/genomes/3492/ ''D. kikkawai'' Genome Assembly Report, NCBI, USA]<br />[http://www.ebi.ac.uk/ena/data/view/GCA_000224215 ''D. kikkawai'' Genome Assembly Report, ENA, UK]
+* <b>''D. melanogaster'' Genome</b>:<br />[https://www.ncbi.nlm.nih.gov/genome/47/ ''D. melanogaster'' Organism Overview, NCBI, USA]<br />[https://www.ncbi.nlm.nih.gov/genome/genomes/47/ ''D. melanogaster'' Genome Assembly Report, NCBI, USA]<br />[http://www.ebi.ac.uk/ena/data/view/GCA_000001215 ''D. melanogaster'' Genome Assembly Report, ENA, UK]
+* <b>''D. miranda'' Genome</b>:<br />[https://www.ncbi.nlm.nih.gov/genome/10915/ ''D. miranda'' Organism Overview, NCBI, USA]<br />[https://www.ncbi.nlm.nih.gov/genome/genomes/10915/ ''D. miranda'' Genome Assembly Report, NCBI, USA]<br />[http://www.ebi.ac.uk/ena/data/view/GCA_000269505 ''D. miranda'' Genome Assembly Report, ENA, UK]
+* <b>''D. mojavensis'' Genome</b>:<br />[https://www.ncbi.nlm.nih.gov/genome/259/ ''D. mojavensis'' Organism Overview, NCBI, USA]<br />[https://www.ncbi.nlm.nih.gov/genome/genomes/259/ ''D. mojavensis'' Genome Assembly Report, NCBI, USA]<br />[http://www.ebi.ac.uk/ena/data/view/GCA_000005175 ''D. mojavensis'' Genome Assembly Report, ENA, UK]
+* <b>''D. navojoa'' Genome</b>:<br />[https://www.ncbi.nlm.nih.gov/genome/45091/ ''D. navojoa'' Organism Overview, NCBI, USA]<br />[https://www.ncbi.nlm.nih.gov/genome/genomes/45091/ ''D. navojoa'' Genome Assembly Report, NCBI, USA]<br />[http://www.ebi.ac.uk/ena/data/view/GCA_001654015 ''D. navojoa'' Genome Assembly Report, ENA, UK]
+* <b>''D. persimilis'' Genome</b>:<br />[https://www.ncbi.nlm.nih.gov/genome/265/ ''D. persimilis'' Organism Overview, NCBI, USA]<br />[https://www.ncbi.nlm.nih.gov/genome/genomes/265/ ''D. persimilis'' Genome Assembly Report, NCBI, USA]<br />[http://www.ebi.ac.uk/ena/data/view/GCA_000005195 ''D. persimilis'' Genome Assembly Report, ENA, UK]
+* <b>''D. pseudoobscura'' Genome</b>:<br />[https://www.ncbi.nlm.nih.gov/genome/219/ ''D. pseudoobscura'' Organism Overview, NCBI, USA]<br />[https://www.ncbi.nlm.nih.gov/genome/genomes/219/ ''D. pseudoobscura'' Genome Assembly Report, NCBI, USA]<br />[http://www.ebi.ac.uk/ena/data/view/GCA_000001765 ''D. pseudoobscura'' Genome Assembly Report, ENA, UK]
+* <b>''D. rhopaloa'' Genome</b>:<br />[https://www.ncbi.nlm.nih.gov/genome/6853/ ''D. rhopaloa'' Organism Overview, NCBI, USA]<br />[https://www.ncbi.nlm.nih.gov/genome/genomes/6853/ ''D. rhopaloa'' Genome Assembly Report, NCBI, USA]<br />[http://www.ebi.ac.uk/ena/data/view/GCA_000236305 ''D. rhopaloa'' Genome Assembly Report, ENA, UK]
+* <b>''D. sechellia'' Genome</b>:<br />[https://www.ncbi.nlm.nih.gov/genome/271/ ''D. sechellia'' Organism Overview, NCBI, USA]<br />[https://www.ncbi.nlm.nih.gov/genome/genomes/271/ ''D. sechellia'' Genome Assembly Report, NCBI, USA]<br />[http://www.ebi.ac.uk/ena/data/view/GCA_000005215 ''D. sechellia'' Genome Assembly Report, ENA, UK]
+* <b>''D. simulans'' Genome</b>:<br />[https://www.ncbi.nlm.nih.gov/genome/200/ ''D. simulans'' Organism Overview, NCBI, USA]<br />[https://www.ncbi.nlm.nih.gov/genome/genomes/200/ ''D. simulans'' Genome Assembly Report, NCBI, USA]<br />[http://www.ebi.ac.uk/ena/data/view/GCA_000259045 ''D. simulans'' Genome Assembly Report, ENA, UK]
+* <b>''D. suzukii'' Genome</b>:<br />[https://www.ncbi.nlm.nih.gov/genome/18317/ ''D. suzukii'' Organism Overview, NCBI, USA]<br />[https://www.ncbi.nlm.nih.gov/genome/genomes/18317/ ''D. suzukii'' Genome Assembly Report, NCBI, USA]<br />[http://www.ebi.ac.uk/ena/data/view/GCA_000472105 ''D. suzukii'' Genome Assembly Report, ENA, UK]<br /> [http://spottedwingflybase.org/ ''D. suzukii'' SpottedWingFlyBase The Spotted Wing Drosophila Project, UC Davis and Oregon State University, USA]
+* <b>''D. takahashii'' Genome</b>:<br />[https://www.ncbi.nlm.nih.gov/genome/3493/ ''D. takahashii'' Organism Overview, NCBI, USA]<br />[https://www.ncbi.nlm.nih.gov/genome/genomes/3493/ ''D. takahashii'' Genome Assembly Report, NCBI, USA]<br />[http://www.ebi.ac.uk/ena/data/view/GCA_000224235 ''D. takahashii'' Genome Assembly Report, ENA, UK]
+* <b>''D. virilis'' Genome</b>:<br />[https://www.ncbi.nlm.nih.gov/genome/261/ ''D. virilis'' Organism Overview, NCBI, USA]<br />[https://www.ncbi.nlm.nih.gov/genome/genomes/261/ ''D. virilis'' Genome Assembly Report, NCBI, USA]<br />[http://www.ebi.ac.uk/ena/data/view/GCA_000005245 ''D. virilis'' Genome Assembly Report, ENA, UK]
+* <b>''D. willistoni'' Genome</b>:<br />[https://www.ncbi.nlm.nih.gov/genome/251/ ''D. willistoni'' Organism Overview, NCBI, USA]<br />[https://www.ncbi.nlm.nih.gov/genome/genomes/251/ ''D. willistoni'' Genome Assembly Report, NCBI, USA]<br />[http://www.ebi.ac.uk/ena/data/view/GCA_000005925 ''D. willistoni'' Genome Assembly Report, ENA, UK]
+* <b>''D. yakuba'' Genome</b>:<br />[https://www.ncbi.nlm.nih.gov/genome/148/ ''D. yakuba'' Organism Overview, NCBI, USA]<br />[https://www.ncbi.nlm.nih.gov/genome/genomes/148/ ''D. yakuba'' Genome Assembly Report, NCBI, USA]<br />[http://www.ebi.ac.uk/ena/data/view/GCA_000005975 ''D. yakuba'' Genome Assembly Report, ENA, UK]]
+=Gene Expression Databases and Tools=
+* <b>BDGP in situ</b>, Patterns of gene expression in Drosophila embryogenesis:<br />[https://insitu.fruitfly.org/cgi-bin/ex/insitu.pl Gene expression database, BDGP, University of California, Berkeley, USA]
+* <b>BGee</b> Normal Gene Expression Data in Animals (based on RNA-Seq, Affymetrix, in situ hybridization, and EST data).<br />[https://www.bgee.org/ SIB, Swiss Institute of Bioinformatics, University of Lausanne, Lausanne, Switzerland]
+* <b>DIGITtally</b>, Finding Genes of Interest DIGITtally: <br /> [https://www.digittally.org/ DIGITtally, University of Glasgow, Glasgow, UK]
+* <b>FlyAtlas2</b>, for exploring how genes are expressed in the tissues of ''D. melanogaster'':<br />[https://flyatlas.gla.ac.uk/FlyAtlas2/index.html FlyAtlas2, University of Glasgow, Glasgow, UK]
+* <b>FlyExpress</b>, an Expression Pattern Search Engine:<br />[http://www.flyexpress.net/ FlyExpress, Arizona State University, USA]
+* <b>Fly-FISH</b>, A Database of Drosophila Embryo mRNA Localizaton Patterns:<br />[https://fly-fish.ccbr.utoronto.ca/ Fly-FISH, University of Toronto, Toronto, Canada]
+* <b>FlyGut-seq</b>, a transcriptomic resource that complements the original [http://flygut.epfl.ch/ Flygut website]:<br />[http://flygutseq.buchonlab.com/ Buchon Lab, Cornell University, Ithaca, NY, USA]
+* <b>FlyLight</b>, Expression Patterns of GAL4, LexA, and Split-GAL4 Driver Lines to enable the visualization and precise manipulation of individual cell types in the Drosophila nervous system:<br />[https://www.janelia.org/project-team/flylight HHMI, Janelia Farms Research Campus]
+* <b>flytrap</b>, a database of P{GAL4} enhancer traps and their expression in brains: <br />[https://www.fly-trap.org/ flytrap, University of Edinburgh, UK]
+* <b>Gene Expression Levels by Cell Line</b> (based on modENCODE data):<br />[https://www.flyrnai.org/cgi-bin/RNAi_expression_levels.pl DRSC/TRiP-FGR, Harvard Medical School, Boston, MA, USA]
+* <b>GEO Profiles</b>, Gene Expression Omnibus:<br />[https://www.ncbi.nlm.nih.gov/geo/info/profiles.html GEO, NCBI, Bethesda, MD USA]
+* <b>MidgutAtlas</b>, Gene expression in five pH-defined regions of the larval midgut of D. melanogaster:<br />[http://flyatlas.gla.ac.uk/MidgutAtlas/index.html Dow laboratory, University of Glascow, Scotland, UK]
+* <b>RNAMiner</b>, A Bioinformatics Protocol for Mining Large RNA-Seq Transcriptomics Data:<br />[https://calla.rnet.missouri.edu/rnaminer/ Cheng Lab, University of Missouri, Mizzou, Columbia, MO, USA]
+=Gene Groups=
+* <b>FlyBase Gene Groups</b>, Manually curated reports on functionally related genes, based on the literature:<br /> [https://flybase.org/lists/FBgg/ Gene group list, FlyBase]
+* <b>FlyBase Signaling Pathways</b>, Manually curated reports on Signaling Pathways, based on the literature:<br /> [https://flybase.org/lists/FBgg/pathways Pathways list, FlyBase]
+* <b>GLAD</b>, an Online Database of Gene List Annotations for Drosophila:<br /> [https://www.flyrnai.org/tools/glad/web/ DRSC/TRiP-FGR, Harvard Medical School, Boston, MA, USA]
+* <b>Interactive fly</b>, Drosophila genes listed by biochemical function:<br /> [https://www.sdbonline.org/sites/fly/aimain/6biochem.htm Interactive Fly, Thomas Brody and Society for Developmental Biology, MD, USA]
+* <b>Interactive fly</b>, Maternally transcribed genes:<br /> [https://www.sdbonline.org/sites/fly/aimain/4matrnl.htm Interactive Fly, Thomas Brody and Society for Developmental Biology, MD, USA]
+* <b>Interactive fly</b>, Zygotically transcribed genes:<br /> [https://www.sdbonline.org/sites/fly/aimain/5zygotic.htm Interactive Fly, Thomas Brody and Society for Developmental Biology, MD, USA]
+* <b>KEGG BRITE</b>, Functional hierarchies and binary relationships of biological entities:<br /> [https://www.genome.jp/kegg/brite.html KEGG, Kyoto University, Kyoto, Japan and University of Tokyo, Tokyo, Japan]
+* <b>UCSC D. melanogaster Gene Sorter</b>, displays tables of genes related by a variety of characteristics including protein-level homology, similarity of gene expression profiles, and genomic proximity.:<br /> [https://genome.ucsc.edu/cgi-bin/hgNear?org=D.+melanogaster UCSC Genome Informatics Group, University of California, Santa Cruz, Santa Cruz, CA, USA]
+=General Bioinformatics Tools=
+* <b>Addgene</b>, Early Career Researcher Toolbox: Free Online Molecular Biology Tools:<br />[https://blog.addgene.org/free-online-molecular-biology-tools Addgene, Watertown, MA, USA]
+* <b>ApE</b>, A plasmid Editor:<br />[https://jorgensen.biology.utah.edu/wayned/ape/ ApE, University of Utah, Salt Lake City, UT, USA]
+* <b>Bioconductor</b>, Open Source Software for Bioinformatics:<br />[https://www.bioconductor.org/ Fred Hutchinson Cancer Research Center, Seattle, USA]
+* <b>Bioz</b>, Insights and recommendations for products, equipment and assays:<br />[https://www.bioz.com/search/Drosophila Palo Alto, CA, USA]
+* <b>Cytoscape</b> -- Network Data Integration, Analysis, and Visualization in a Box:<br />[https://cytoscape.org/ Cytoscape, Cytoscape Consortium, Canada, France, and USA]
+* <b>FlyMine</b>, an Integrated Database for Drosophila and Anopheles Genomics:<br />[https://www.flymine.org/ University of Cambridge, United Kingdom]
+* <b>FlyNet</b>, a network prioritization server for Drosophila melanogaster biology:<br />[http://www.inetbio.org/flynet/ NetBioLab, Yonsei University, Seoul, Korea]
+=Gene Set Enrichment Analysis=
+A summary table of selected GSEA tools with information about set up can be found [[FlyBase:GSEA|<b>here</b>]]
+* <b>DAVID</b>, Database for Annotation, Visualization and Integrated Discovery :<br />[https://david.ncifcrf.gov/ DAVID, Laboratory of Human Retrovirology and Immunoinformatics, Frederick, MD, USA]]
+* <b>Enrichr</b>, Human and Mouse Gene Set Enrichment Analysis:<br />[https://maayanlab.cloud/Enrichr/ Enrichr, Center for Bioinfomatics, Mount Sinai, New York, NY, USA]
+* <b>MOET</b>, Multi Ontology Enrichment Tool:<br />[https://rgd.mcw.edu/rgdweb/enrichment/start.html MOET, Rat Genome Database]
+* <b>modEnrichr</b>, Model Organism Gene Set Enrichment Analysis:<br />[https://maayanlab.cloud/modEnrichr/ modEnrichr, Center for Bioinfomatics, Mount Sinai, New York, NY, USA]
+* <b>flyEnrichr</b>, D.melanogaster Gene Set Enrichment Analysis:<br />[https://maayanlab.cloud/FlyEnrichr/ flyEnrichr, Center for Bioinfomatics, Mount Sinai, New York, NY, USA]
+* <b>GO term finder</b>, Generic GO Term Finder:<br />[https://go.princeton.edu/cgi-bin/GOTermFinder GOTERMFINDER, Lewis-Sigler Institute for Integrative Genomics, Princeton University, New Jersey, NJ, USA]
+* <b>GOC</b>, GO Enrichment Analysis:<br />[https://geneontology.org/ Gene Ontology Consortium]
+* <b>GSEA</b>, Gene Set Enrichment Analysis:<br />[https://www.gsea-msigdb.org/gsea/index.jsp GSEA, Broad Institute, Cambridge, MA, USA]
+* <b>g:Profiler</b>, g:Profiler/g:GOSt:<br />[https://biit.cs.ut.ee/gprofiler/gost g:Profiler, Institute of Computer Science, University of Tartu, Tartu, Estonia]
+* <b>GOrilla</b>, Gene Ontology enRIchment anaLysis and visuaLizAtion tool:<br />[https://cbl-gorilla.cs.technion.ac.il/ GOrilla, Technion, Israel Institute of Technology, Israel]
+* <b>PANGEA</b>, PAthway, Network and Gene-set Enrichment Analysis:<br />[https://www.flyrnai.org/tools/pangea/ PANGEA, DRSC, Harvard Medical School, Boston, MA, USA]
+* <b>PANTHER</b>, PANTHER GO Enrichment Analysis:<br />[https://pantherdb.org/ PANTHER, University of Southern California, Los Angeles, CA, USA]
+* <b>REVIGO</b>, Reduce + Visualize Gene Ontology:<br />[http://revigo.irb.hr/ REVIGO, Division of electronics, Ruđer Bošković Institute, Zagreb, Croatia]
+* <b>ShinyGO</b>, ShinyGO 0.80:<br />[http://bioinformatics.sdstate.edu/go80/ ShinyGO, South Dakota State University, Brookings, SD, USA]
+* <b>WebGestalt</b>, WebGestalt Gene Set Enrichment Analysis:<br />[https://www.webgestalt.org/  WebGestalt, Baylor College of Medicine, Houston, TX, USA]
+=Genome Sequencing Projects=
+* <b>''D. pseudoobscura'' genome project</b>:<br />[https://www.hgsc.bcm.edu/arthropods/drosophila-pseudoobscura-genome-project D. pseudoobscura Human Genome Sequencing Center, Baylor College of Medicine, USA]
+=Human Disease: Drosophila Models and Orthologous Genes=
+* <b>AGR</b> -- Alliance of Genome Resources:<br />[https://www.alliancegenome.org/ Alliance of Genome Resources, RGD, MGD, ZFIN, FlyBase, WormBase, SGD, GO consortium, USA and UK]
+* <b>Bloomington Stock Center</b>, Drosophila and Human Disease page:<br />[https://bdsc.indiana.edu/stocks/hd/index.html Bloomington Stock Center, Bloomington, IN, USA]
+* <b>DIOPT-DIST</b>, Disease-related Ortholog Tool:<br />[http://www.flyrnai.org/cgi-bin/DRSC_DG_query.pl DRSC-TRiP-FGR, Harvard Medical School, Boston, MA, USA]
+* <b>Drosophila as a Model for Human Diseases</b>:<br />[https://www.sdbonline.org/sites/fly/modelsystem/aamodelsystem.htm Interactive Fly, Bethesda, MD, USA]
+* <b>Drosophila Models of Human Disease</b>, a blog by Stephanie Mohr and Annette Parks:<br />[http://flydiseasemodels.blogspot.com/ flydiseasemodels.blogspot.com/] <br />
+* <b>FlyNet Human Disease Prioritization</b>:<br /> [http://www.inetbio.org/flynet/Network_fly_comm.php NetBioLab, Yonsei University, Seoul, Korea]
+* <b>Gene2Function</b>:<br /> [http://www.gene2function.org/search/ Gene2Function, Harvard Medical School, Boston, MA, USA]
+* <b>HuDis</b>, high confidence human disease gene - fly gene ortholog pairs:<br />[https://fgr.hms.harvard.edu/hudis-trip-fly-stocks DRSC/TRiP-FGR, Harvard Medical School, Boston, MA, USA]
+* <b>MARRVEL</b>, Model organism Aggregated Resources for Rare Variant ExpLoration:<br />[http://marrvel.org/ MARRVEL, Baylor College of Medecine, Houston, TX, USA]
+* <b>MORPHIN</b>, Model ORganism Projected on a Human Integrated gene Network:<br />[http://www.inetbio.org/morphin/index.php MORPHIN, Lee Lab, Yonsei University, Korea and Marcotte Lab, University of Texas at Austin, USA.]
+=Interaction and Pathway Databases=
+* <b>BioCyc - FLY</b> -- Curated Drosophila melanogaster Pathways:<br />[https://biocyc.org/FLY/organism-summary?object=FLY FlyCyc, Harvard University, Cambridge, USA]
+* <b>BioGRID</b>, The General Repository for Interaction Datasets:<br />[https://thebiogrid.org/index.php BioGRID, Mount Sinai Hospital, Toronto, Canada]
+* <b>COMPLEAT</b>, protein COMPLex Enrichment Analysis Tool:<br />[https://www.flyrnai.org/compleat/ COMPLEAT, DRSC, Harvard Medical School, Boston, MA, USA]
+* <b>DPiM</b>, Drosophila Protein interaction Map:<br/>[https://interfly.med.harvard.edu/ DPiM, Harvard University Medical School, Boston, MA, USA]
+* <b>DroID</b>, Drosophila Interactions Database:<br />[http://www.droidb.org/ Drosophila Interaction Database, Detroit, USA]
+* <b>FlyBase Signaling Pathways</b>, Manually curated reports on Signaling Pathways, based on the literature:<br /> [http://flybase.org/lists/FBgg/pathways Pathways list, FlyBase]
+* <b>FlyNet Gene Prioritization</b>: <br /> [http://www.inetbio.org/flynet/Network_gene_prioritization.php NetBioLab, Yonsei University, Seoul, Korea]
+* <b>FlyOde</b>, FLY Organ Developmental Network: <br /> [http://flyode.boun.edu.tr/index.html FlyOde, Bogazici University, Istanbul, Turkey]
+* <b>HOMER</b>, Software for motif discovery and next-gen sequencing analysis: <br /> [http://homer.ucsd.edu/homer/motif/ HOMER, University of California at San Diego, San Diego, CA, USA]
+* <b>IM Browser</b>, Drosophila Interactions Database:<br />[http://proteome.wayne.edu/PIMdb.html IM Browser, Wayne State University, Detroit, MI, USA]
+* <b>IntAct</b>, Molecular Interaction Database:<br />[https://www.ebi.ac.uk/intact/ IntAct, EMBL-EBI, Hinxton, UK]
+* <b>KEGG</b> -- Kyoto Encyclopedia of Genes and Genomes:<br />[https://www.genome.jp/kegg/ KEGG, Kyoto, Japan]
+* <b>MIST</b> -- Molecular Interactions Search Tool:<br />[https://fgrtools.hms.harvard.edu/MIST/ MIST, Harvard Medical School, Boston, MA, USA]
+* <b>Reactome Pathway Database</b>:<br />[https://reactome.org/ Reactome, OICR, Ontario, Canada, EMBL-EBI, UK, NYU Medical Center, NY, USA]
+* <b>SignaLink</b>, an integrated resource to analyze signaling pathway cross-talks, transcription factors, miRNAs and regulatory enzymes.:<br />[http://signalink.org/ SignaLink, Earlham Institute, Norwich, UK]
+* <b>STRING</b>, Known and Predicted Protein-Protein Interactions<br />[https://string-db.org/ STRING, SIB, Switzerland CPR, Denmark, and EMBL, Heidelberg, Germany]
+* <b>WikiPathways</b>, an open, public platform dedicated to the curation of biological pathways by and for the scientific community:<br />[https://www.wikipathways.org/index.php/WikiPathways WikiPathways, Gladstone Institute, San Francisco, CA, USA and Maastricht University, The Netherlands]
+=Metabolomics=
+* <b>FlyMet</b>, A Tissue- and Sex-Specific Metabolomic Atlas and Database :<br />[http://www.flymet.org/ FlyMet, University of Glasgow, Glasgow, Scotland]
+=Miscellaneous=
+* <b>AGR</b> -- Alliance of Genome Resources:<br />[https://www.alliancegenome.org/ Alliance of Genome Resources, RGD, MGD, ZFIN, FlyBase, WormBase, SGD, GO consortium, USA and UK]
+* <b>BioLitMine</b>, Biological Literature Mining Tool for Human and Model Organisms:<br />[https://www.flyrnai.org/tools/biolitmine/web/ BioLitMine, Harvard Medical School, Boston, MA, USA]
+* <b>Bionet Archives</b>, a collection of bionet USENET newsgroups and parallel e-mail lists regarding Drosophila:<br />[http://www.bio.net/hypermail/dros/ Genome Informatics Lab, Indiana University, Bloomington, Indiana, USA]
+* <b>Drosophila App</b>, A mobile application developed by Genesee for use in fly research: <br />[https://play.google.com/store/apps/details?id=kaver.co.drosophila&hl=en Android]
+* <b>Drosophila Information Service</b>:<br />[https://www.ou.edu/journals/dis/ DIS, Norman, Oklahoma, USA]
+* <b>Drosophila Species Photographs</b>, Photographs of 133 species of Drosophila:<br />[https://kyotofly.kit.jp/cgi-bin/ehime/photo_data_list.cgi Ehime University, Matsuyama, Japan]
+* <b>Drosophila Workers Unite! A laboratory manual for working with Drosophila</b>:<br />[https://marksteinlab.org/dwu/ Michele Markstein Lab, UMass Amherst, Amherst, MA, USA]
+* <b>The Encyclopedia of North American Drosophilids Volume 1: Drosophilids of the Midwest and Northeast</b>:<br />[https://digitalcommons.mtu.edu/oabooks/1/ by T. Werner, Michigan Technological University, Tessa Steenwinkel, Michigan Technological University, and J.Jaenike, University of Rochester]
+* <b>Fly Art</b> - A compendium of arty imagery, sculptures or poetry inspired by Drosophila or flies in the wider sense.:<br />[https://droso4public.wordpress.com/fly-art/ University of Manchester, Manchester, UK]
+* <b>Fly Labs and References</b>, a large list of fly labs and recent publications: <br />[https://www.sdbonline.org/sites/fly/flylabs/a.html Interactive Fly, Bethesda, MD, USA]
+* <b>FlyTree</b>, the Drosophila Researcher Genealogy has been incorporated into the Academic Tree Project: <br />[https://academictree.org/flytree/ FlyTree, USA]
+* <b>Fully automated drosophila wing landmarking</b>, Automatically finds more than 110 landmark points and creates a digital twin of the drosophila wing:<br />[https://datamarkin.com/models/drosophila-wings-beta/ Datamarkin, Marseille, France]
+* <b>GenAge</b> -- The Ageing Gene Database:<br />[https://genomics.senescence.info/genes/index.html Human Ageing Genomic Resources, Institute of Integrative Biology, Liverpool, UK]
+* <b>Gene Lookup</b>, Gene and Reagent Lookup:<br />[https://www.flyrnai.org/cgi-bin/DRSC_gene_lookup.pl Gene Lookup, DRSC, Harvard Medical School, Boston, MA, USA]
+* <b>GlyCosmos Portal</b>, a Web portal aiming to integrate the glycosciences with the life sciences. It consists of Standards, Repositories and Data Resources, providing information about genes, proteins, lipids, pathways and diseases.:<br />[https://glycosmos.org/ GlyCosmos, GlyCosmos is a member of the GlySpace Alliance, consisting of ExPASy Glycomics, GlyCosmos, and GlyGen]
+* <b>Interactive Fly</b>, A cyberspace guide to Drosophila development and metazoan evolution<br />[https://www.sdbonline.org/sites/fly/aimain/1aahome.htm Interactive Fly, Bethesda, MD, USA]
+* <b>Manchester Fly Facility, Resources</b> - A compendium of information on ''Drosophila melanogaster'' as a model organism:<br />[https://droso4public.wordpress.com/resources/ University of Manchester, Manchester, UK]
+* <b>Multiplex Fluorescent mRNA <em>In Situ</em> Hybridization</b>, information on how to perform multiplex fluorescent mRNA in situ hybridization on Drosophila embryos: <br />[http://people.biology.ucsd.edu/davek/ Bier and McGinnis Labs, UCSD, San Diego, California, USA]
+* <b>What's hot today:</b> Current papers in developmental biology and gene function:<br />[https://www.sdbonline.org/sites/fly/aimain/model-organisms-this-week.htm Interactive Fly, Bethesda, MD, USA]
+* <b>The WWW Virtual Library--Drosophila</b>:<br />[https://www.ceolas.org/fly/ Drosophila Virtual Library]
+=Non-coding (ncRNA) Databases and Tools=
+==General==
+* <b>NONCODE</b>, An integrated knowledge database dedicated to ncRNAs, especially lncRNAs:<br />[http://www.noncode.org/ NONCODE, Tsinghua University and Chinese Academy of Sciences, Beijing, China]
+* <b>Rfam</b>, A collection of RNA sequence families of structural RNAs including non-coding RNA genes as well as cis-regulatory elements :<br />[https://rfam.org/ Rfam, EMBL-EBI, Hinxton, UK]
+* <b>RNAcentral</b>, Integrated access to a comprehensive and up-to-date set of non-coding RNA sequences provided by a collaborating group of Expert Databases :<br />[https://rnacentral.org/ RNAcentral, EMBL-EBI, Hinxton, UK]
+==lncRNA==
+* <b>LncRBase V.2</b>, a database of information about lncRNAs from 8 species (human, mouse, fly, zebrafish, rat, chicken, C.elegans and cow) :<br />[http://dibresources.jcbose.ac.in/zhumur/lncrbase2/index_Contact.php LncRBase, Bose Institute, West Bengal, India]
+==miRNA==
+===General===
+* <b>miRBase</b>, A searchable database of published miRNA sequences and annotations (current miBase release is 22 - last updated 2018):<br />[https://mirbase.org/// miRBase, University of Manchester, UK]<br />
+::NOTE - mirBase Release 21 (June 2014) uses old reference genome assemblies for D. melanogaster (Dmel_Release_5), D. simulans (Dsim_Release_1) and D. pseudoobscura (Dpse_Release_2). Linkouts from D. melanogaster miRNA genes to the Ensembl Genome browser (which displays Dmel_Release_6) will point to the old "Release_5" coordinates, which will be off the mark for many genes, especially those on X, 2R, 3R and 4 chromosomes.
+* <b>miRNEST</b>, An integrated collection of miRNA predictions from high-throughput sequencing experiments and external database annotations (last updated 2015):<br />[http://rhesus.amu.edu.pl/mirnest/copy/ miRNEST, The Adam Mickiewicz University in Poznan, Poznan, Poland]
+* <b>TransmiR</b>, A database of transcription factor-microRNA regulation (last updated 2018):<br />[http://www.cuilab.cn/transmir TransmiR], Peking University Health Science Center, Peking, Chin
+===miRNA Target Prediction===
+* <b>DIANA microT-CDS</b>, MicroRNA Target Prediction:<br />[https://dianalab.e-ce.uth.gr/html/dianauniverse/index.php?r=microT_CDS DIANA Tools, DIANA LAB, Athens, Greece]
+* <b>MinoTar</b>, Predict microRNA Targets in Coding Sequence (last updated 2010):<br />[https://www.flyrnai.org/cgi-bin/DRSC_MinoTar.pl MinoTar, DRSC, Harvard Medical School, Boston, MA, USA]
+* <b>TargetScanFly</b>, Prediction of microRNA targets based on miRNA seed region and target conservation (last updated 2012):<br />[https://www.targetscan.org/fly_12/ TargetScanFly, Whitehead Institute and MIT Dept. of Biology, Cambridge, MA, USA]
+===Validated miRNA Targets===
+* <b>DIANA TarBase</b>, MicroRNA Target Database (last updated 2017):<br />[https://dianalab.e-ce.uth.gr/html/diana/web/index.php?r=tarbasev8 DIANA TarBase, DIANA LAB, Athens, Greece]
+* <b>miRTex</b>, A text-mining system that extracts miRNA-gene regulation relations and miRNA-target relations from literature (last updated 2017):<br />[https://research.bioinformatics.udel.edu/miRTex/ miRTex, University of Delaware, Newark, DE, USA]
+===Comparative miRNA Analysis===
+* <b>microRNAviewer</b>, A global view of homologous miRNA genes in many species (last updated 2012):<br />[http://people.csail.mit.edu/akiezun/microRNAviewer/index.html microRNAviewer, Tel Aviv University, Tel Aviv, Israel]
+==rRNA==
+* <b>SILVA</b>, High quality ribosomal RNA databases (last updated 2020):<br />[https://www.arb-silva.de/ SILVA, Max Planck Institute for Marine Microbiology and Jacobs University, Bremen, Germany]
+==tRNA==
+* <b>tRFdb</b>, A relational database of Transfer RNA related Fragments:<br />[http://genome.bioch.virginia.edu/trfdb/index.php tRFdb, Dutta lab, University of Virginia, Charlottesville, VA, USA]
+==snoRNA==
+* <b>snOPY</b>, a snoRNA orthological gene database providing comprehensive information about snoRNAs, snoRNA gene loci and target RNAs.:<br />[http://snoopy.med.miyazaki-u.ac.jp/ snOPY, University of Miyazaki, Japan ]
+==SRP RNA==
+* <b>SRPDB</b>, Signal Recognition Particle Database:<br />[http://rth.dk/resources/rnp/SRPDB/SRPDB.html SRPDB, University of Texas Health Science Center, San Antonio, USA]
+=Ontology Resources=
+* <b>BioPortal</b>, a biomedical ontologies repository and browser:<br />[http://bioportal.bioontology.org/ BioPortal, The National Center for Biomedical Ontology, USA]
+* <b>Disease Ontology (DO)</b>, ontology of disease terms:<br />[http://disease-ontology.org/ Disease Ontology]
+* <b>Gene Ontology Consortium (GO)</b><br />[https://geneontology.org/ Gene Ontology Consortium]
+* <b>GOrilla</b> -- Gene Ontology enRIchment and anaLysis and viuaLizAtion tool:<br />[https://cbl-gorilla.cs.technion.ac.il/ GOrilla, Israel]
+* <b>OboEdit</b>, browser for OBO ontologies:<br />[http://oboedit.org/ OboEdit]
+* <b>The OBO Foundry</b>, an ontology registry:<br />[http://obofoundry.org/ OboFoundry]
+* <b>Ontobee</b>, an ontologies browser:<br />[https://ontobee.org/ Ontobee, He Group, University of Michigan Medical School, Ann Arbor, Michigan, USA]
+* <b>OLS - Ontology Lookup Service</b>, an ontologies browser:<br />[https://www.ebi.ac.uk/ols4/ Ontology Lookup Service, EMBL-EBI, Hinxton, UK]
+* <b>Protege</b>, browser for OWL ontologies:<br />[https://protege.stanford.edu/ Protege, Stanford Center for Biomedical Informatics Research, Stanford University School of Medicine, USA]
+* <b>QuickGO</b>, a browser for Gene Ontology terms and annotations:<br />[https://www.ebi.ac.uk/QuickGO/ QuickGO, EMBL-EBI, Hinxton, UK]
+=Orthology Predictions=
+* <b>Compara</b>, Ensembl Compara provides cross-species resources and analyses, at both the sequence level and the gene level.<br />[http://useast.ensembl.org/info/genome/compara/index.html?redirect=no Ensembl, Hinxton, UK]
+* <b>DIOPT</b>, DRSC Integrative Ortholog Prediction Tool<br />[https://www.flyrnai.org/cgi-bin/DRSC_orthologs.pl DRSC/TRiP-FGR, Harvard Medical School, Boston, MA, USA]
+* <b>DIOPT-DIST: DIOPT Diseases and Traits</b>, DRSC Disease Gene Query Tool:<br />[https://www.flyrnai.org/cgi-bin/DRSC_DG_query.pl DRSC/TRiP-FGR, Harvard Medical School, Boston, MA, USA]
+* <b>EggNOG</b>, A database of orthologous groups and functional annotation:<br />[http://eggnogdb.embl.de/ Computational Biology Group, EMBL, Heidelberg, Germany]
+* <b>Gene2Function</b>:<br /> [https://www.gene2function.org/search/ Gene2Function, Harvard Medical School, Boston, MA, USA]
+* <b>Hieranoid</b>, An orthology inference method using a hierarchical approach. Hieranoid performs pairwise orthology analysis using InParanoid at each node in a guide tree as it progresses from its leaves to the root.<br />[https://hieranoid.sbc.su.se/index.html Hieranoid, Stockholm Bioinformatics Centre, Stockholm, Sweden]
+* <b>HieranoiDB</b>, An online database of orthologs inferred by Hieranoid 2 for a representative set of proteomes.<br />[https://hieranoidb.sbc.su.se/ HieranoiDB, Stockholm Bioinformatics Centre, Stockholm, Sweden]
+* <b>Homologene</b>, An automated system for constructing putative homology groups from the complete gene sets of a wide range of eukaryotic species.<br />[https://www.ncbi.nlm.nih.gov/datasets/gene/ NCBI, Bethesda, MD, USA]
+* <b>InParanoiDB 9</b>, Ortholog groups with inparalogs for proteins and protein domains<br />[https://inparanoidb.sbc.su.se/about/ InParanoiDB 9, Stockholm Bioinformatics Centre, Stockholm, Sweden]
+* <b>Isobase</b>, A Database of Functionally Related Orthologs, which incorporates PPI network data in addition to sequence similarity.<br />[http://cb.csail.mit.edu/cb/mna/isobase/ MIT, Cambridge, MA, USA]
+* <b>MARRVEL</b>, Model organism Aggregated Resources for Rare Variant ExpLoration:<br />[http://marrvel.org/ MARRVEL, Baylor College of Medecine, Houston, TX, USA]
+* <b>OMA Browser</b>, The OMA (“Orthologous MAtrix”) project is a method and database for the inference of orthologs among complete genomes.<br />[https://omabrowser.org/oma/home/ Nucl. Acids Res. 43 (D1): D240-D249. doi: 10.1093/nar/gku1158]
+* <b>OrthoDB</b>, The Hierarchical Catalog of Orthologs<br />[https://www.orthodb.org/ Zdobnov Computational Evolutionary Genomics group, University of Geneva, Geneva, Switzerland]
+* <b>OrthoFinder</b>, A comprehensive platform for comparative genomics that finds orthogroups and orthologs, infers rooted gene trees for all orthogroups and identifies all of the gene duplication events.<br />[http://www.stevekellylab.com/software/orthofinder University of Oxford, Oxford, UK]
+* <b>OrthoInspector</b>, A software suite for inference of orthologous relationships between protein coding-genes and an online resource to access and query precomputed orthology databases.<br />[https://lbgi.fr/orthoinspector/ ICube Laboratory, Graffenstaden, France]
+* <b>OrthoMCL</b>, Ortholog Groups of Protein Sequences<br />[https://orthomcl.org/orthomcl/ EuPathDB]
+* <b>PANTHER</b>, PANTHER Classification System<br />[http://pantherdb.org/genes/ Thomas Lab, University of Southern California, Los Angeles, CA, USA]
+* <b>PhylomeDB</b>, PhylomeDB is a public database for complete catalogs of gene phylogenies (phylomes)<br />[http://phylomedb.org/ Comparative Genomics Groups at CRB, Barcelona, Spain]
+* <b>Roundup</b>, A large-scale orthology database using the Reciprocal Smallest Distance (RSD) algorithm.<br />[https://wall-lab.stanford.edu/projects/roundup/ Wall lab, Stanford University, Palo Alto, CA, USA]
+* <b>TreeFam</b>, A database composed of phylogenetic trees inferred from animal genomes. It provides orthology/parology predictions as well the evolutionary history of genes.<br />[http://www.treefam.org/ EMBL-EBI, Hinxton, UK]
+=Phylogenetic Comparison Tools=
+* <b>DIOPT</b>, DRSC Integrative Ortholog Prediction Tool:<br />[https://www.flyrnai.org/cgi-bin/DRSC_orthologs.pl DRSC/TRiP-FGR, Harvard Medical School, Boston, MA, USA]
+* <b>HomoloGene</b> -- automated system fo constructing putative homology groups:<br />[https://www.ncbi.nlm.nih.gov/datasets/gene/ NCBI, Bethesda, MA, USA]
+* <b>InParanoiDB 9</b>, Ortholog groups with inparalogs for proteins and protein domains<br />[https://inparanoidb.sbc.su.se/about/ InParanoiDB 9, Stockholm Bioinformatics Centre, Stockholm, Sweden]
+* <b>MANTiS</b>, a phylogenetic framework for multi-species genome comparisons:<br />[https://www.mantisdb.org/MANTiS/Welcome.html MANTiS, UniversitÃ© Libre de Bruxelles, Belgium]
+* <b>OrthoDB</b>, the Hierarchical Catalog of Orthologs:<br />[http://www.orthodb.org/ OrthoDB, University of Geneva, Switzerland]
+* <b>Vista Tools</b> -- Whole Genome Comparative Analysis of the ''D. melanogaster'' (CAF1) Genome:<br />[https://pipeline.lbl.gov/cgi-bin/gateway2?bg=droMel_caf1&selector=vistapoint Whole Genome Comparative Analysis of the D. melanogaster (CAF1) Genome, LBNL, USA]
+=Population Biology and Polymorphism Resources=
+* <b>BDGP Single Nucleotide Polymorphism (SNP) Project</b>:<br />[https://www.fruitfly.org/SNP/ Berkeley Drosophila Genome Project, University of California, Berkeley, USA]
+* <b>Drosophila Genetics Reference Panel</b>:<br />[https://www.hgsc.bcm.edu/arthropods/drosophila-genetic-reference-panel DGRP, Baylor College of Medicine, Houston, TX and NC State University, Raleigh, NC USA]
+* <b>Drosophila Genetics Reference Panel 2</b>:<br />[http://dgrp2.gnets.ncsu.edu/ DGRP2, NC State University, Raleigh, NC and Baylor College of Medicine, Houston, TX, USA]
+* <b>Drosophila Genome Nexus</b>: a population genomic resource that provides ''D. melanogaster'' genomes from multiple sources<br />[http://www.johnpool.net/genomes.html University of Wisconsin, Madison, WI, USA]
+* <b>DSPR</b>, Drosophila Synthetic Population Resource:<br />[https://wfitch.bio.uci.edu/~dspr/index.html DSPR, University of Kansas and UC Irvine, USA]
+* <b>Global Diversity Lines</b>: a Five Continent Reference Panel of Sequenced Drosophila melanogaster Strains<br />[https://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?study=SRP050151 Global Diversity Lines, Cornell University, Ithaca, NY, USA]
+=Protein Analysis and Modification=
+* <b>AlphaFold Protein Structure Database</b>, AlphaFold DB provides open access to protein structure predictions; An AI system developed by DeepMind that predicts a protein’s 3D structure from its amino acid sequence:<br />[https://alphafold.ebi.ac.uk/ EMBL-EBI, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK]
+* <b>ExPASy</b>, the SIB Bioinformatics Resource Portal which provides access to scientific databases and software tools in different areas of life sciences:<br />[https://www.expasy.org/ SIB Swiss Institute of Bioinformatics, Genève, Switzerland]
+* <b>GPCRDB</b>, information system for G protein-coupled receptors (GPCRs):<br />[https://gpcrdb.org/ GPCRDB, The GPCRDB (G Protein-Coupled Receptor Data Base) partnership]
+* <b>InterPro</b> protein domain analysis of Drosophila:<br />[http://www.ebi.ac.uk/interpro/ InterPro: protein sequence analysis & classification, EBI, UK]
+* <b>iProteinDB</b> Integrated Protein Database of Post Translational Modifications for Drosophila Genes:<br />[https://www.flyrnai.org/tools/iproteindb/web/ iProteinDB, Harvard Medical School, Boston, MA, USA]
+* <b>MEROPS</b>, an information resource for peptidases:<br />[https://www.ebi.ac.uk/merops/ MEROPS, Wellcome Trust Sanger Institute, Hinxton, UK]
+* <b>ModBase</b>, Database of Comparative Protein Structure Models:<br />[https://modbase.compbio.ucsf.edu/modbase-cgi/index.cgi ModBase, UCSF, San Francisco, CA, USA]
+* <b>Panther (Protein Analysis THrough Evolutionary Relationships)</b> protein classification system:<br />[https://www.pantherdb.org/ Panther Protein Classification System, Applied Biosystems &amp; Celera, USA]
+* <b>PDB</b>, Protein Data Bank:<br />[https://www.rcsb.org/ PDB, The Research Collaboratory for Structural Bioinformatics (RCSB) consortium]
+* <b>PhospoPep</b>, Protein Phosphorylation Database: <br />[http://phosphopep.org/ Institute for Systems Biology, Seattle, Washington, USA]
+* <b>ProteinProspector</b>, a proteomics tools for mining sequence databases in conjunction with Mass Spectrometry experiments: <br />[https://prospector.ucsf.edu/prospector/mshome.htm UCSF Mass Spectrometry Facility, San Francisco, California, USA]
+* <b>RBPDB</b>, the database of RNA-binding protein specificities:<br />[http://rbpdb.ccbr.utoronto.ca/ RBPDB]
+* <b>SMART</b>, Simple Modular Architecture Research Tool:<br />[http://smart.embl-heidelberg.de/ SMART, Protein Domain Analysis, EMBL, Heidleberg]
+* <b>UniProtKB</b>, a comprehensive catalog of information on proteins:<br />[https://www.uniprot.org/ UniProtKB, The UniProt Consortium]
+=Public Education=
+* <b>About the history of Drosophila research</b>, An extensive collection of media pertaining to the history of fruit fly research: <br />[https://droso4public.wordpress.com/history/ Manchester Fly Facility, University of Manchester, UK]
+* <b>droso4schools</b>, An online resource for school lessons using the fruit fly Drosophila:<br />[https://droso4schools.wordpress.com/ Manchester Fly Facility, University of Manchester, UK]
+* <b>''Drosophila'' & Computer Programming Game</b>, A scratch computer game based on the Drosophila life cycle: <br /> [https://poppi62.wordpress.com/2015/08/28/school-flies/#ICT Manchester Fly Facility, University of Manchester, UK]
+* <b>Experiments with Drosophila for Biology Courses</b>, An e-resource book for laboratory experiments at under- and post-graduate levels and for research projects in Biology courses :<br />[https://www.ias.ac.in/Publications/e-Books/Experiments_with_Drosophila_for_Biology_Courses Indian Academy of Sciences, India] [http://ftp.flybase.org/flybase/associated_files/Experiments_with_Drosophila_for_Biology_Courses.pdf pdf here ]
+* <b>FlyMove</b>, an Image, Movie and Interactive Shockwave Resource:<br />[http://flymove.uni-muenster.de/ FlyMove, Muenster, Germany]
+* <b>Lay articles</b>, A collection of lay articles about fly research: <br />[https://droso4public.wordpress.com/lay-articles/ Manchester Fly Facility, University of Manchester, UK]
+* <b>Manchester Fly Facility Public Resource Page</b>:<br />[https://droso4public.wordpress.com/ Manchester Fly Facility, University of Manchester, UK]
+=RNAi=
+* <b>DRSC-TRiP-FGR</b>, DRSC/TRiP Functional Genomics Resources:<br />[https://fgr.hms.harvard.edu/ DRSC-TRiP-FGR, Harvard Medical School, Boston, MA, USA]
+* <b>Search by gene(s) to find hit information for genes and DRSC amplicons in DRSC screens</b>:<br /> [https://www.flyrnai.org/RNAi_find_hit_info.html DRSC-TRiP-FGR, Harvard Medical School, Boston, MA, USA]
+* <b>FlyRNAi blog</b>, a DRSC resource concerning RNAi, cell-based assays, <i>Drosophila</i> cell culture, high-throughput screening, & fly biology:<br />[http://flyrnai.blogspot.com/ flyrnai.blogspot.com]
+* <b>Fosmid rescue analysis tool</b> for identification of fosmids appropriate for cross-species rescue of RNAi:<br />[https://www.flyrnai.org/cgi-bin/RNAi_find_rescue_compl.pl DRSC-TRiP-FGR, Harvard Medical School, Boston, MA, USA]
+* <b>GenomeRNAi</b>, Heidelberg, a database of RNA interference (RNAi) screens:<br />[http://www.genomernai.org GenomeRNAi, DKFZ, Heidelberg, Germany]
+* <b>GESS</b>, off-target RNAi prediction:<br />[https://www.flyrnai.org/gess/ DRSC-TRiP-FGR, Harvard Medical School, Boston, MA, USA]
+* <b>Predicted Off-Target Free Sequence Regions</b>:<br />[https://www.flyrnai.org/RNAi_find_frag_free.html DRSC-TRiP-FGR, Harvard Medical School, Boston, MA, USA]
+* <b>RNAiCut</b>, Automated Detection of Significant Genes from Functional Genomic Screens:<br /> [https://cb.csail.mit.edu/cb/RNAiCut/ Berger Lab, MIT, Boston, MA, USA]
+* <b>RSVP</b>, RNAi Stock Validation & Phenotypes:<br />[https://fgr.hms.harvard.edu/rsvp DRSC-TRiP-FGR, Harvard Medical School, Boston, MA, USA]
+* <b>SnapDragon</b>, RNAi Design:<br />[https://www.flyrnai.org/cgi-bin/RNAi_find_primers.pl DRSC-TRiP-FGR, Harvard Medical School, Boston, MA, USA]
+* <b>TRiP</b>, Transgenic RNAi Project: <br />[https://fgr.hms.harvard.edu/fly-in-vivo-rnai DRSC-TRiP-FGR, Harvard Medical School, Boston, MA, USA]
+* <b>Tsinghua Fly Center</b>, THFC RNAi Stock Collection for triggering RNAi in soma and germline: <br />[https://thfc.zzbd.org/en THFC, Tsinghua Fly Center, Beijing, China]
+* <b>UP-TORR Fly</b>, a tool for identifying updated targets of RNAi reagents: <br />[https://www.flyrnai.org/up-torr/ Updated Targets of RNAi Reagents, DRSC-TRiP-FGR, Harvard Medical School, Boston, MA, USA]
+* <b>VDRC</b>, Vienna Drosophila Resource Center: <br />[https://shop.vbc.ac.at/vdrc_store/ Genome-wide transgenic Drosophila RNAi libraries, VDRC, Vienna, Austria]
-=Genetic and Protein Interaction Databases=
 =Sequence Analysis=
-=Atlases, Images, and Videos=
+* <b>DCPD</b> -- Drosophila Core Promoter Database, A list of 205 Drosophila melanogaster core promoters aligned by their empirically determined transcription start site: <br />[http://labs.biology.ucsd.edu/Kadonaga/DCPD.htm Kadonaga Lab, UCSD, San Diego, California, USA]
-=Other=
+* <b>FlyPrimerBank</b>, a comprehensive qPCR primer database for Drosophila: <br />[https://www.flyrnai.org/FlyPrimerBank FlyPrimerBank, DRSC, Harvard Medical School, Boston, MA, USA]
+* <b>FGENESH</b>, Annotation of animal genomes-genes, promoters, functional motifs, protein sub-cellular localization: <br />[http://www.softberry.com/berry.phtml?topic=case_study_animal&no_menu=on Annotation of genomes, Softberry, USA]
+* <b>Gemme</b>, A fast, scalable and simple method to predict mutational landscapes from natural sequences: <br />[http://www.lcqb.upmc.fr/GEMME/Home.html Gemme, Sorbonne University, Paris, France]
+* <b>GenePalette</b>, a tool for genome sequence visualization and navigation: <br />[http://www.genepalette.org/ GenePalette, University of California, San Diego, USA]
+* <b>Genie Gene finder for Drosophila: </b>:<br />[https://www.fruitfly.org/seq_tools/genie.html Genie, Berkeley Drosophila Genome Project, University of California, Berkeley, USA]
+* <b>HRMA</b> -- High Resolution Melt Analysis: <br /> [https://fgr.hms.harvard.edu/hrma HRMA, DRSC, Harvard Medical School, Boston, MA, USA]
+* <b>MEME Suite</b> -- Motif-based Sequence Analysis Tools: <br />[http://meme-suite.org/ MEME, U. of Queensland, U. of Washington, USA, UCSD, SDSC, NBCR, CBRC, and National Center for Research Resources]
+* <b>RepeatMasker</b>: <br />[https://www.repeatmasker.org/ RepeatMasker Institute for Systems Biology, Seattle, WA, USA]
+* <b>Splice Site Prediction for Drosophila</b>:<br />[https://www.fruitfly.org/seq_tools/splice.html Splice Site Prediction, Berkeley Drosophila Genome Project, University of California, Berkeley, USA]
+* <b>Web Apollo</b>, a collaborative genomic annotation editor: <br />[http://apollo.berkeleybop.org/ Web Apollo, LBL, Berkeley, USA]
+=Single Cell RNA-seq=
+* <b>ASAP</b> Automated Single-cell Analysis Pipeline: <br />[https://asap.epfl.ch/ ASAP, EPFL, Lausanne, Switzerland, Swiss Institute of Bioinformatics, Lausanne, Switzerland]
+* <b>cisTopic</b> Probabilistic modelling of cis-regulatory topics from single cell epigenomics data: <br />[https://github.com/aertslab/cisTopic/ cisTopic, VIB Center for Brain & Disease Research, Leuven, Belgium, Department of Human Genetics, KU Leuven, Leuven, Belgium]
+* <b>DeepCMC</b> A Neural Networks (NN) based approach for identifying genes that contain spatial information: <br />[https://github.com/TJU-CMC-Org/SingleCell-DREAM DeepCMC, Thomas Jefferson University, Philadelphia, PA, USA]
+* <b>Distmap</b> To spatially map single cell RNA sequencing data by using an existing reference database of in situs: <br />[https://github.com/rajewsky-lab/distmap Distmap, BIMSB and MDC, Berlin, Germany]
+* <b>DRscDB</b> DRSC scRNA-seq DataBase: <br />[https://www.flyrnai.org/tools/single_cell/ DRscDB, DRSC, Harvard Medical School, Boston, USA]
+* <b>DVEX</b> Drosophila Virtual Expression eXplorer: <br />[https://shiny.mdc-berlin.de/DVEX/ DVEX, BIMSB and MDC, Berlin, Germany]
+* <b>Fly Cell Atlas</b> A consortium of Drosophila researchers interested in single-cell genomics, transcriptomics, and epigenomics: <br />[https://flycellatlas.org/ Fly Cell Atlas, Founders - Stein Aerts, Leuven, Belgium, Bart Deplancke, Lausanne, Switzerland, Robert Zinzen, Berlin, Germany]
+* <b>Lasso.TopX</b> An approach using the Lasso and ranking statistics for identifying genes that contain spatial information: <br />[https://github.com/TJU-CMC-Org/SingleCell-DREAM/ Lasso.TopX, Thomas Jefferson University, Philadelphia, PA, USA]
+* <b>novoSpaRc</b> Predicts locations of single cells in space by solely using single-cell RNA sequencing data.: <br />[https://github.com/rajewsky-lab/novosparc novoSpaRc, Harvard and Broad Institute, Cambridge, MA, USA, Max Delbrück Center, Berlin, Germany]
+* <b>SCEA</b> Single Cell Expression Atlas - Single Cell Gene Expression Across Species: <br />[https://www.ebi.ac.uk/gxa/sc SCEA, EMBL-EBI, Hinxton, UK, Sanger Institute, Wellcome Genome Campus, Hinxton, UK, Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK]
+* <b>SCENIC</b> Single-Cell Regulatory Network Inference and Clustering <br />[https://github.com/aertslab/SCENIC SCENIC, Center for Brain & Disease Research, Leuven, Belgium, KU Leuven, Leuven, Belgium, University of Liege, Liege, Belgium, VIB Center for Cancer Biology, Leuven, Belgium]
+* <b>SCope</b> Fast Visualization Tool for Large-Scale and High Dimensional Single-Cell Data <br />[https://github.com/aertslab/SCope SCope, VIB KU Leuven, Leuven, Belgium]
+* <b>Seurat</b> An R package designed for QC, analysis, and exploration of single-cell RNA-seq data.: <br />[https://satijalab.org/seurat/ Seurat, NYU, NY, NY, USA]
+* <b>VSN</b> A Repository of Pipelines for Single-Cell Data Analysis in Nextflow DSL2:  <br />[https://github.com/vib-singlecell-nf/vsn-pipelines VSN-Pipelines]
+=Taxonomy=
+* <b>FlyPhenomics</b>, phenotypic differences between species of the ''D. melanogaster'' subgroup:<br />[http://www.normalesup.org/~vorgogoz/FlyPhenomics/ FlyPhenomics, Paris, France]
+* <b>TaxoDros</b> Drosophilidae Taxonomic Database:<br />[https://bioinfo.museum.hokudai.ac.jp/ Drosophilidae Taxonomic Database, Japan]
+* <b>TaxoDros</b>, the database on Taxonomy of Drosophilidae:<br />[http://www.taxodros.uzh.ch/ TaxoDros, University of Zurich, Switzerland]
+* <b>Taxonomy</b>, NCBI Taxonomy Database:<br />[https://www.ncbi.nlm.nih.gov/taxonomy NCBI, Bethesda, MD USA]
+* <b>Taxonomy of Drosophilidae - JDD - Japan Drosophila Database</b> <br />[http://www.drosophila.jp/jdd/index_en.html Japan Drosophila Database (JDD) on Taxonomy, Japan]
+=Transcription Regulation Databases and Tools=
+* <b>CIS-BP</b>, The online library of transcription factors and their DNA binding motifs:<br />[http://cisbp.ccbr.utoronto.ca/ CIS-BP, Hughes Lab, University of Toronto, Toronto, Canada and Weirauch lab, Cincinnati Children's Hospital, Cincinnati, OH, USA]
+* <b>EPD</b>, the Eukaryotic Promoter Database:<br />[https://epd.expasy.org/epd EPD, Epalinges s/Lausanne, Switzerland]
+* <b>Fly Factor Survey</b> - Database of Drosophila TF DNA-binding Specificities: <br />[http://pgfe.umassmed.edu/ffs/ FLy Factor Survey, UMass Medical School, Worcester, MA, USA]
+* <b>FlyReg</b>, DNase I Footprint Database - retired<br />[http://www.flyreg.org/ University of Manchester Bioinformatics Resources, University of Manchester, UK]
+* <b>JASPAR</b>, A database of transcription factor (TF) binding profiles stored as position frequency matrices and TF flexible models for TFs across multiple species.<br />[https://jaspar.elixir.no/ JASPAR]
+* <b>Neural Network Promoter Prediction for Drosophila</b>:<br />[https://www.fruitfly.org/seq_tools/promoter.html Neural Network Promoter Prediction, Berkeley Drosophila Genome Project, University of California, Berkeley, CA, USA]
+* <b>OnTheFly</b>, Database of Drosophila Transcription Factors and Transcription Factor Binding Sites <br />[https://bhapp.c2b2.columbia.edu/OnTheFly/index.php OnTheFly, Columbia University, NY, USA]
+* <b>REDfly</b>, Regulatory Element Database for Drosophila:<br />[http://redfly.ccr.buffalo.edu/ REDfly, University at Buffalo, New York, Buffalo, NY, USA]
+* <b>ReMap</b>, a large-scale integrative analysis of DNA-binding experiments for Homo sapiens, Mus musculus, Dropshiphila melanogaster, and Arabadopsis thaliana transcriptional regulators based on manual curation of ChIP-seq, ChIP-exo, DAP-seq from public sources:<br />[https://remap.univ-amu.fr/ ReMap, TAGC Inserm, Marseille, France]
+* <b>FlyTF.org</b>, The Drosophila Transcription Factor Database:<br />[https://www.mrc-lmb.cam.ac.uk/genomes/FlyTF/old_index.html FlyTF.org, MRC Cambridge, UK]
+* <b>scEnhancer</b>, A database of single cell enhancer annotation in human, mouse, and fly:<br />[http://enhanceratlas.net/scenhancer/ scEnhancer, Sun Yat-sen University, Shenzhen, China and Johns Hopkins University, Baltimore, MD, USA]
+* <b>TRANSFAC</b>, A database of transcription factors and their binding sites:<br />[http://gene-regulation.com/pub/databases.html#transfac TRANSFAC, Braunschweig, Germany]
+* <b>UniPROBE</b>, Universal PBM (protein binding microarray) Resource for Oligonucleotide Binding Evaluation:<br />[http://thebrain.bwh.harvard.edu/uniprobe/ UniPROBE, Bulyk lab, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA]
+=Suggest a tool or resource=
+*Please [http://flybase.org/contact/email contact Flybase] to suggest a tool or resource for the list.
+[[Category:DONE]]

Difference between revisions of "FlyBase:Drosophila Online Resources"

Latest revision as of 13:33, 19 March 2024

Atlases, Images and Videos

Cell Lines and Cell Culture

CRISPRs and TALENs

Data Repositories

DNA Reagents

Drosophila Genomes Data and Metadata

Gene Expression Databases and Tools

Gene Groups

General Bioinformatics Tools

Gene Set Enrichment Analysis

Genome Sequencing Projects

Human Disease: Drosophila Models and Orthologous Genes

Interaction and Pathway Databases

Metabolomics

Miscellaneous

Non-coding (ncRNA) Databases and Tools

General

lncRNA

miRNA

General

miRNA Target Prediction

Validated miRNA Targets

Comparative miRNA Analysis

rRNA

tRNA

snoRNA

SRP RNA

Ontology Resources

Orthology Predictions

Phylogenetic Comparison Tools

Population Biology and Polymorphism Resources

Protein Analysis and Modification

Public Education

RNAi

Sequence Analysis

Single Cell RNA-seq

Taxonomy

Transcription Regulation Databases and Tools

Suggest a tool or resource

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