Revision as of 17:55, 25 July 2018

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
BDTNP, A cellular resolution 3D gene expression and morphology Atlas of the blastoderm:
Berkeley Drosophila Transcription Network Project, University of California, Berkeley, USA
BrainTrap, A collection of 3D confocal datasets taken from EYFP expressing protein trap Drosophila lines from the Cambridge Protein Trap project:
Armstrong Lab, University of Edinburgh, Edinburgh, UK
CSIRO Anatomical Atlas of Flies:
CSIRO Entomology, Australia
FlyBase Maps, A collection of illustrated and electron micrograph maps of polytene chromosomes for the 12 originally sequenced Drosophila species:
FlyBase Maps
FlyCircuit, a Database of Drosophila Brain Neurons:
FlyCircuit, National Tsing Hua University, Taiwan
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
Interactive Maps: four maps displaying markers and lineages of D. melanogaster neuroblasts, glial cells, and interneurons:
Interactive Maps, Institut fur Genetik, Johannes Gutenberg University, Mainz, Germany
Jove, videos of experimental techniques:
Jove, Journal of Visualized Experiments, USA
Learning to Fly, a poster showing photographs of commonly used marker phenotypes in D. melanogaster:
Genesis (Journal), Wiley Online Library
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

CRISPRs and TALENs

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:
Schier Lab, Harvard University, Cambridge, MA, Church Lab, Harvard Medical School, Boston, MA, USA
CRISPOR Model organism gRNA design tool:
TEFOR, Gif-sur-Yvette, France
CRISPR/Cas Web Resources Web Resources for design and planning of CRISPR/Cas9 studies:
IGTRCN, Insect Genetic Technologies Research Coordination Network, University of Maryland, Rockville, MD, USA
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 Genome Engineering Resources CRISPR Design Tool:
Zhang Lab, MIT, Boston, MA, USA
CRISPR fly design -- reagents, protocols, and results from fly CRISPR/Cas experiments:
Bullolk Lab, MRC Laboratory of Molecular Biology, Cambridge, UK
CRISPRscan Novel scoring algorithm for selecting sgRNAs
Giraldez Lab, Yale University, New Haven, CT, USA
DRSC CRISPR Efficiency Tool for Assessment of Designs:
DRSC/TRiP-FGR, Harvard Medical School, Boston, MA, USA
DRSC Finding CRISPRs, Drosophila CRISPR gRNA design search tool:
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, Resource Site:
O'Connor-Giles, Wildonger, and Harrison Labs, University of Wisconsin-Madison, WI, USA
flyCRISPR, Optimal 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
OXfCRISPR, Oxford Fly CRISPR Resources:
Liu lab, University of Oxford, Oxford, UK
SIFTED, Specificity Inference for TAL Effector Design:
Bulyk Lab, Harvard Medical School, Boston, MA, USA
TALengineering.org, A Comprehensive Resource for Engineered TAL Effector Technology:
Ekker lab, Joung Lab, MGH, Boston, USA
ZiFiT Targeter, Tool for Identifying Zinc Finger Nuclease Sites in Specific Target Sequences:
MGH and Harvard Medical School, Boston, MA

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
Ensembl Genome Browser:
EMBL-EBI, Hinxton, UK
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 Map 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

Drosophila Genomes Data and Metadata

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
BDTNP, A cellular resolution 3D gene expression and morphology Atlas of the blastoderm.
Berkeley Drosophila Transcription Network Project, 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
Flannotator, Annotation of Gene Expression:
FlyAnnotator, University of Cambridge, UK
FlyAtlas2, for exploring how genes are expressed in the tissues of D. melanogaster:
FlyAtlas2, University of Glasgow, Glasgow, UK
FlyEx, a Database of Segmentation Gene Expression in Drosophila:
FlyEx, St. Petersburg State Polytechnical University, Russia
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 Driver Lines:
HHMI, Janelia Farms Research Campus
FlyOde, FLY Organ Developmental Network:
FlyOde, Bogazici University, Istanbul, Turkey
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
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
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

Bioconductor, Open Source Software for Bioinformatics:
Fred Hutchinson Cancer Research Center, Seattle, USA
BioMart, Data Warehouse:
BioMart, EMBL-EBI, OICR, SRSI
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
DNA & Protein Work List, A list of tools aggregated by the Prokop Lab:
http://www.prokop.co.uk/Links/tools.html
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
Galaxy: Open Source Bioinformatics Tools:
Galaxy, Penn State, PA USA and Emory University, GA USA
GSEA, Gene Set Enrichment Analysis:
GSEA, Broad Institute, Cambridge, MA, USA

Genome Sequencing Projects

D. pseudoobscura genome project:
D. pseudoobscura Human Genome Sequencing Center, Baylor College of Medicine, USA
D. simulans genome project:
D. simulans White 501 Genome Sequencing Center, Washington University, USA
D. yakuba genome project:
D. yakuba Genome Sequencing Center, Washington University, USA
D. simulans and yakuba sequencing projects:
DPGP, University of California, Davis, USA

Human Disease: Drosophila Models and Orthologous Genes

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
HuDis, high confidence human disease gene - fly gene ortholog pairs:
DRSC/TRiP-FGR, Harvard Medical School, Boston, MA, 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.
NeuroGeM, A knowledgebase of genetic modifiers in neurodegenerative diseases:
CHiBi, The University of British Columbia, Vancouver, BC, Canada

Interaction and Pathway Databases

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
DAPPER, database for protein-protein interactions:
DAPPER, University of Cambridge, Cambridge, UK
DPiM, Drosophila Protein interaction Map:
Harvard University Medical School, Boston, MA, USA
DroID, Drosophila Interactions Database:
Drosophila Interaction Database, Detroit, USA
Drosophila PIMRider, Drosophila Protein Interaction Map:
Drosophila PIMRider, Hybrigenics, Paris, France
FlyCyc -- Curated Drosophila melanogaster Pathways:
FlyCyc, Harvard University, Cambridge, USA
FlyNet Gene Prioritization:
NetBioLab, Yonsei University, Seoul, Korea
FlyOde, FLY Organ Developmental Network:
FlyOde, Bogazici University, Istanbul, Turkey
FlyReactome -- a Curated Knowledgebase of Drosophila melanogaster Pathways:
FlyReactome, University of Cambridge, Cambridge, UK
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
Reactome Pathway Database:
Reactome, OICR, Ontario, Canada, EMBL-EBI, UK, NYU Medical Center, NY, USA
SignedPPI, Searchable Database of Known and Predicted Protein-protein Interactions:
DRSC, Harvard Medical School, Boston, MA, USA
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

Laboratory Resources

Laboratory Manual of Drosophila:
PDF, Chippindale, A. et al., Department of Ecology & Evolutionary Biology, University of California, Irvine, USA

Miscellaneous

Bionet Archives, a collection of bionet USENET newsgroups and parallel e-mail lists regarding Drosophila:
Genome Informatics Lab, Indiana University, Bloomington, Indiana, USA
DOR, Database of Olfactory Receptors:
DOR, NCBS, Bangalore, India, AIST, Tokyo, Japan
Drosophila App, A mobile application developed by Genesee for use in fly research:
iTunes | Android
Drosophila Information Service:
DIS, Norman, Oklahoma, USA
Drosophilids of the Midwest and Northeast:
by T. Werner, Michigan Technological University and J.Jaenike, University of Rochester
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
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
IGTRCN, Insect Genetic Technologies Research Coordination Network:
IGTRCN, University of Maryland, Rockville, MD, USA
Interactive Fly, A cyberspace guide to Drosophila development and metazoan evolution
Interactive Fly, Bethesda, MD, USA
Jfly, a data depository for the fly and other insects, with an emphasis for the Japanese-speaking fly community:
Jfly, University of Tokyo, Japan
Manchester Fly Facility, Outreach resources - A compendium of information on Drosophila melanogaster as a model organism:
University of Manchester, Manchester, UK
MitoDrome, Drosophila melanogaster nuclear genes encoding for mitochondrial proteins:
MitoDrome, Bari, Italy
Mitotic Spindle Assembly Database:
Genes Required for Mitotic Spindle Assembly in S2 cells, University of California, San Francisco, USA
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
PhospoPep -- phosphorylation site data from D. melanogaster cell lines:
The Aebersold group at the ETH in collaboration with the FGCZ in Switzerland, and the ISB, 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 (last updated 2017):
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 (last updated 2017):
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 (last updated 2017):
RNAcentral, EMBL-EBI, Hinxton, UK

lncRNA

lncrnadb, Long Noncoding RNA Database (last updated 2015):
lncrnadb, University of New South Wales, Sydney, Australia
LNCediting, Function of RNA editing in lncRNAs (last updated 2016):
LNCediting, Huazhong University of Science and Technology, Wuhan, China and University of Texas, Houston, Texas, USA

miRNA

General

miRBase, A searchable database of published miRNA sequences and annotations (last updated 2014):
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
Tools4miRs, Manually curated platform gathering methods for the broadly-defined miRNA analysis (last updated 2017):
Tools4miRs, Polish Academy of Sciences and University of Warsaw, Warsaw, Poland
TransmiR, A database of transcription factor-microRNA regulation (last updated 2013):
[http://www.cuilab.cn/transmir TransmiR, Peking University Health Science Center, Peking, Chin

miRNA Target Prediction

DIANA microT-CDS, MicroRNA Target Prediction (last updated 2014):
DIANA microT-CDS, DIANA LAB, Athens, Greece
MicroCosm Targets, Computationally predicted targets for microRNAs across many species based on MiRanda algorithm (last updated 2007):
MicroCosm Targets, EMBL-EBI, Hinxton, UK
microRNA.org, Predicted microRNA targets & target downregulation scores based on miRanda and mirSVR algorithms (last updated 2007):
microRNA.org, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
MinoTar, Predict microRNA Targets in Coding Sequence (last updated 2010):
MinoTar, DRSC, Harvard Medical School, Boston, MA, USA
miRNA - Target Gene Prediction (last updated 2005):
miRNA - Target Prediction, EMBL, Heidelberg, Germany
miRNA_Targets (last updated 2011):
miRNA targets on full length mRNAs, Deakin University, Victoria, Australia
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 2014):
DIANA TarBase, DIANA LAB, Athens, Greece
miRecords, A database of experimentally validated miRNA targets curated from literature (last updated 2009):
miRecords, University of Minnesota, Minneapolis, MN, USA
miRTarBase, Experimentally Validated microRNA-target Interactions Database (last updated 2015):
miRTarBase, ISBLab, Hsinchu, Taiwan
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

CoGemiR, Comparative Genomics Analysis of MicroRNA (last updated 2008):
CoGemiR, Telethon Institute of Genetics and Medicine, Naples, Italy
microRNAviewer, A global view of homologous miRNA genes in many species (last updated 2012):
microRNAviewer, Tel Aviv University, Tel Aviv, Israel
miROrtho, Predictions of precursor miRNA genes covering several animal genomes combining orthology and a Support Vector Machine (last updated 2009):
miROrtho, University of Geneva, Geneva, Switzerland

rRNA

SILVA, High quality ribosomal RNA databases (last updated 2016):
SILVA, Max Planck Institute for Marine Microbiology and Jacobs University, Bremen, Germany

tRNA

GtRNAdb, tRNAscan-SE analysis of complete genomes:
GtRNAdb, Lowe lab, University of California, Santa Cruz, Santa Cruz, CA, USA
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

AmiGO 2, tools for searching and browsing the Gene Ontology database:
AmiGO 2, Berkeley Bioinformatics Open-source Projects, USA
BioPortal, a biomedical ontologies repository and browser:
BioPortal, The National Center for Biomedical Ontology, USA
Disease Ontology, ontology of disease terms:
Disease Ontology
Gene Ontology Consortium
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
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
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
Inparanoid, InParanoid: ortholog groups with inparalogs
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
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
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
EvoPrinter, Identification of Evolutionarily Resilient DNA Sequences
NINDS, NIH, Bethesda MD, USA
HomoloGene -- automated system fo constructing putative homology groups:
NCBI, Bethesda, MA, USA
InParanoid, Eukaryotic Ortholog Groups:
InParanoid, Karolinska Institute, 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
flyDIVaS, a comparative genomics database resource of Drosophila divergence and selection:
Temple University, Philadelphia, PA, USA
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
Drosophila Polymorphism Database:
DPDB, Universitat Autonoma de Barcelona, Barcelona, Spain
DPGP, Drosophila Population Genomics Project:
DPGP, University of California, Davis, USA
DSPR, Drosophila Synthetic Population Resource:
DSPR, University of Kansas and UC Irvine, USA
FlySNP Project:
FlySNP, Austrian Academy of Sciences, Austria
FlyVar Project: A Database of Drosophila Genetics Variations
FlyVar, Fudan University, Shanghai, China and Baylor College of Medicine, Houston, TX, USA
Global Diversity Lines: a Five Continent Reference Panel of Sequenced Drosophila melanogaster Strains
Global Diversity Lines, Cornell University, Ithaca, NY, USA

Protein Analysis

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
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, interactive interrogation of MS-derived phosphorylation data from 4 different organisms:
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
Fly on the Wall, a blog by Bethany Christmann regarding fruit flies and research:
Griffith Lab, Brandeis University, Waltham, MA, USA
FlyMove, an Image, Movie and Interactive Shockwave Resource:
FlyMove, Muenster, Germany
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 hits 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, Transgenic RNAi lines:
Center of Biomedical Analysis, Tsinghua University, 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
EvoPrinterHD, A "High Definition" view of conserved DNA:
NINDS, NIH, Bethesda, MD, 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
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

Taxonomy

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

Transcription Regulation Databases and Tools

BDTNP, ChIP/chip in vivo DNA binding data:
Berkeley Drosophila Transcription Network Project, University of California, Berkeley, USA
CORE, A database utilizing the ElemeNT algorithm (see below) to annotate individual Drosophila observed TSS (using either CAGE or RNAseq data) for the presence of the various core promoter elements:
Juven-Gershon Lab, Bar-Ilan University, Ramat-Gan, Israel
DBD, Transcription factor prediction database:
DBD, MRC, Cambridge, UK
ElemeNT, An interactive tool for rapid and convenient detection of core promoter elements within a given sequence, implemented in Perl programming language:
Juven-Gershon Lab, Bar-Ilan University, Ramat-Gan, Israel

EPD, the Eukaryotic Promoter Database:
EPD, Epalinges s/Lausanne, Switzerland
Fly Factor Survey - Database of Drosophila TF DNA-binding Specificitiies:
FLy Factor Survey, UMass Medical School, Worcester, MA, USA
FlyReg, DNase I Footprint Database:
University of Manchester Bioinformatics Resources, University of Manchester, UK
i-cisTarget, An integrative genomics method for the prediction of regulatory features and cis-regulatory modules in Human, Mouse, and Fly:
i-cisTarget, University of Leuven, Leuven, Belgium
Neural Network Promoter Prediction for Drosophila:
Neural Network Promoter Prediction, Berkeley Drosophila Genome Project, University of California, Berkeley, USA
OnTheFly, Database of Drosophila Transcription Factors and Transcription Factor Binding Sites
OnTheFly, Columbia University, USA
REDfly, Regulatory Element Database for Drosophila:
REDfly, University at Buffalo, New York, USA
The Drosophila Transcription Factor Database:
FlyTF.org, MRC Cambridge, UK
TRANSFAC, A database of transcription factors and their binding sites:
TRANSFAC, Braunschweig, Germany

Suggest a tool or resource

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

@@ Line 2: / Line 2: @@
 * <b>Atlas of Drosophila Development</b>, An Atlas following the main events of embryogenesis and post-embryonic development:<br />[http://www.sdbonline.org/sites/fly/atlas/00atlas.htm Volker Hartenstein and Interactive Fly, Bethesda, MD, USA]
 * <b>BDTNP</b>, A cellular resolution 3D gene expression and morphology Atlas of the blastoderm:<br />[http://bdtnp.lbl.gov/Fly-Net/bioimaging.jsp?w=summary Berkeley Drosophila Transcription Network Project, University of California, Berkeley, USA]
-* <b>BrainTrap</b>, a collection of 3D confocal datasets taken from EYFP expressing protein trap Drosophila lines from the Cambridge Protein Trap project: <br />[http://fruitfly.inf.ed.ac.uk/braintrap/ Armstrong Lab, University of Edinburgh, Edinburgh, UK]
+* <b>BrainTrap</b>, A collection of 3D confocal datasets taken from EYFP expressing protein trap Drosophila lines from the Cambridge Protein Trap project: <br />[http://fruitfly.inf.ed.ac.uk/braintrap/ Armstrong Lab, University of Edinburgh, Edinburgh, UK]
 * <b>CSIRO</b> Anatomical Atlas of Flies:<br />[http://www.ento.csiro.au/biology/fly/fly.html# CSIRO Entomology, Australia]
-* <b>Electron micrograph maps</b> of ''D. melanogaster'' polytene chromosomes:<br />[http://www.helsinki.fi/~saura/EM/index.html Sorsa Maps, Helsinki, Finland]
+* <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]
-* <b>FlyBrain</b>, an Online Atlas and Database of the Drosophila Nervous System:<br />[http://flybrain.neurobio.arizona.edu/ FlyBrain, University of Arizona, Tucson, USA]
 * <b>FlyCircuit</b>, a Database of Drosophila Brain Neurons:<br />[http://www.flycircuit.tw/ FlyCircuit, National Tsing Hua University, Taiwan]
-* <b>FlyGut</b>, An interactive Database that aims to provide a comprehensive atlas of the Drosophila melanogaster adult midgut (see also, [http://flygutseq.buchonlab.com/ FlyGut-seq]):<br />[http://flygut.epfl.ch/ Buchon Lab, Cornell University, Ithaca, NY, USA & Lemaitre Lab, EPFL, Lausanne, Switzerland]
 * <b>FlyMove</b>, an Image, Movie and Interactive Shockwave Resource:<br />[http://flymove.uni-muenster.de/ FlyMove, Muenster, Germany]
 * <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]
@@ Line 14: / Line 12: @@
 * <b>Interactive Maps</b>: four maps displaying markers and lineages of ''D. melanogaster'' neuroblasts, glial cells, and interneurons:<br />[http://www.genetik.biologie.uni-mainz.de/106.php Interactive Maps, Institut fur Genetik, Johannes Gutenberg University, Mainz, Germany]
 * <b>Jove</b>, videos of experimental techniques:<br />[http://www.jove.com/index/browse.stp?Search=Drosophila Jove, Journal of Visualized Experiments, USA]
-* <b>Learning to Fly</b>, a poster describing marker phenotypes in the fruit fly:<br />[http://onlinelibrary.wiley.com/journal/10.1002/%28ISSN%291526-968X/homepage/free_posters.htm Genesis (Journal), Wiley Online Library]
+* <b>Learning to Fly</b>, a poster showing photographs of commonly used marker phenotypes in D. melanogaster:<br />[http://onlinelibrary.wiley.com/journal/10.1002/%28ISSN%291526-968X/homepage/free_posters.htm Genesis (Journal), Wiley Online Library]
 * <b>PeptideAtlas</b>, a multi-organism, publicly accessible compendium of peptides identified in a large set of tandem mass spectrometry proteomics experiments: <br />[http://www.peptideatlas.org/ Seattle Proteome Center, Seattle, Washington, USA]
-* <b>Scans of Bridges</b>' original 1935 polytene drawings for ''D. melanogaster''<nowiki>:</nowiki><br />[http://www.hawaii.edu/bio/Chromosomes/poly/poly.html GEM Website, University of Hawaii, USA]
 * <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]
 =CRISPRs and TALENs=
-* <b>Cas9 Design</b>:<br />[http://cas9.cbi.pku.edu.cn/ Center for Bioinformatics, Peking University, Peking, China]
 * <b>CCTop</b> CRISPR/Cas9 optimum target finder:<br />[http://crispr.cos.uni-heidelberg.de/ Center for Organismal Studies, Heidelberg University, Heidelberg, DE]
-* <b>CHOPCHOP</b> CRISPR/Cas9 target online predictor, mammalian and other major model organisms including fly:<br />[https://chopchop.rc.fas.harvard.edu/about.php/ Schier Lab, Harvard University, Cambridge, MA, Church Lab, Harvard Medical School, Boston, MA, USA]
+* <b>CHOPCHOP</b> CRISPR/Cas9 target online predictor, mammalian and other major model organisms including fly:<br />[http://chopchop.cbu.uib.no// Schier Lab, Harvard University, Cambridge, MA, Church Lab, Harvard Medical School, Boston, MA, USA]
 * <b>CRISPOR</b> Model organism gRNA design tool:<br />[http://tefor.net/crispor/crispor.cgi/ TEFOR, Gif-sur-Yvette, France]
 * <b>CRISPR/Cas Web Resources</b> Web Resources for design and planning of CRISPR/Cas9 studies:<br />[http://igtrcn.org/knowledgebase/crisprcas-web-resources// IGTRCN, Insect Genetic Technologies Research Coordination Network, University of Maryland, Rockville, MD, USA]
@@ Line 37: / Line 33: @@
 * <b>Genome Engineering by CRISPR/Cas9 in Drosophila</b>:<br />[http://www.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>OXfCRISPR</b>, Oxford Fly CRISPR Resources:<br />[http://groups.mrcfgu.ox.ac.uk/liu-group/useful-links/oxfcrispr/oxfcrispr Liu lab, University of Oxford, Oxford, UK]
+* <b>OXfCRISPR</b>, Oxford Fly CRISPR Resources:<br />[https://www.dpag.ox.ac.uk/research/liu-group/liu-group-news/oxfcrispr Liu lab, University of Oxford, Oxford, UK]
-* <b>SIFTED</b>, Specificity Inference for TAL Effector Design:<br />[http://thebrain.bwh.harvard.edu/software.html Bulyk Lab, Harvard Medical School, Boston, MA, USA]
+* <b>SIFTED</b>, Specificity Inference for TAL Effector Design:<br />[http://ec2-54-88-183-115.compute-1.amazonaws.com/ Bulyk Lab, Harvard Medical School, Boston, MA, USA]
-* <b>TAL Effectors</b>:<br />[http://taleffector.genome-engineering.org/ Zhang lab, MIT, Boston, MA, 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>ZiFiT Targeter</b>, Tool for Identifying Zinc Finger Nuclease Sites in Specific Target Sequences:<br />[http://zifit.partners.org/ZiFiT/ MGH and Harvard Medical School, Boston, MA]
@@ Line 49: / Line 44: @@
 * <b>EMBL-EBI</b>, The European Bioinformatics Institute:<br />[http://www.ebi.ac.uk/ EMBL-EBI, Hinxton, UK]
 * <b>ENA</b>, European Nucleotide Archive:<br />[http://www.ebi.ac.uk/embl/ 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>Ensembl Genome Browser</b>:<br />[http://useast.ensembl.org/index.html EMBL-EBI, Hinxton, UK]
 * <b>Gene Disruption Project (GDP)</b>:<br />[http://flypush.imgen.bcm.tmc.edu/pscreen/ GDP, Baylor College of Medicine, Texas]<br />[http://flypush.imgen.bcm.tmc.edu/pscreen/transposons.html Schematic drawings of Transposons]
-* <b>GenBank</b>,the NIH genetic sequence database:<br />[http://www.ncbi.nlm.nih.gov/Genbank/ GenBank, NCBI, Bethesda, MD USA]
+* <b>GenBank</b>,the NIH genetic sequence database:<br />[http://www.ncbi.nlm.nih.gov/Genbank/ GenBank, NCBI, Bethesda, USA]
-* <b>GEO Datasets</b>, Gene Expression Omnibus:<br />[http://www.ncbi.nlm.nih.gov/geo/info/datasets.html NCBI, Bethesda, MD USA]
+* <b>GEO Datasets</b>, Gene Expression Omnibus:<br />[http://www.ncbi.nlm.nih.gov/geo/info/datasets.html NCBI, Bethesda, USA]
-* <b>NCBI</b>, National Center fo Biotechnology Information:<br />[http://www.ncbi.nlm.nih.gov Bethesda, MD 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 Map Viewer</b>, A genome view of Drosophila melanogaster:<br />[http://www.ncbi.nlm.nih.gov/mapview/map_search.cgi?taxid=7227 NCBI, Bethesda, MD USA]
+* <b>NCBI</b>, National Center for Biotechnology Information:<br />[http://www.ncbi.nlm.nih.gov Bethesda, MD USA]
-* <b>PubMed</b>, Biomedical literature full-text archive:<br />[http://www.ncbi.nlm.nih.gov/pubmed PubMed, NCBI, Bethesda, MD USA]
+* <b>NCBI Map Viewer</b>, A genome view of Drosophila melanogaster:<br />[http://www.ncbi.nlm.nih.gov/mapview/map_search.cgi?taxid=7227 NCBI, Bethesda, USA]
-* <b>PubMed Central</b>, Biomedical literature citations and abstracts:<br />[http://www.ncbi.nlm.nih.gov/pmc/ PubMed Central, NCBI, Bethesda, MD USA]
+* <b>PubMed</b>, Biomedical literature full-text archive:<br />[http://www.ncbi.nlm.nih.gov/pubmed PubMed, NCBI, Bethesda, USA]
+* <b>PubMed Central</b>, Biomedical literature citations and abstracts:<br />[http://www.ncbi.nlm.nih.gov/pmc/ PubMed Central, NCBI, Bethesda, USA]
 * <b>SRA</b>, Sequence Read Archive:<br />[http://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, 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]
 =Drosophila Genomes Data and Metadata=
@@ Line 85: / Line 82: @@
 * <b>''D. sechellia'' Genome</b>:<br />[http://www.ncbi.nlm.nih.gov/genome/271/ ''D. sechellia'' Organism Overview, NCBI, USA]<br />[http://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 />[http://www.ncbi.nlm.nih.gov/genome/200/ ''D. simulans'' Organism Overview, NCBI, USA]<br />[http://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 />[http://www.ncbi.nlm.nih.gov/genome/18317/ ''D. suzukii'' Organism Overview, NCBI, USA]<br />[http://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]
+* <b>''D. suzukii'' Genome</b>:<br />[http://www.ncbi.nlm.nih.gov/genome/18317/ ''D. suzukii'' Organism Overview, NCBI, USA]<br />[http://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 />[http://www.ncbi.nlm.nih.gov/genome/3493/ ''D. takahashii'' Organism Overview, NCBI, USA]<br />[http://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 />[http://www.ncbi.nlm.nih.gov/genome/261/ ''D. virilis'' Organism Overview, NCBI, USA]<br />[http://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]
@@ Line 95: / Line 92: @@
 * <b>BDTNP</b>, A cellular resolution 3D gene expression and morphology Atlas of the blastoderm.<br />[http://bdtnp.lbl.gov/Fly-Net/bioimaging.jsp?w=summary Berkeley Drosophila Transcription Network Project, 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 />[http://bgee.org/ SIB, Swiss Institute of Bioinformatics, University of Lausanne, Lausanne, Switzerland]
-* <b><em>cis</em>Patterns</b>, A database of over 100 Drosophila GAL4-driver lines regulated by single cis-regulatory enhancers:<br />[http://cispatterns.ninds.nih.gov/ Jermaine Ross and the Odenwald Lab, NINDS, NIH, Bethesda MD, USA]
 * <b>Flannotator</b>, Annotation of Gene Expression:<br />[http://www.flyprot.org/index.php FlyAnnotator, University of Cambridge, UK]
 * <b>FlyAtlas2</b>, for exploring how genes are expressed in the tissues of ''D. melanogaster'':<br />[http://flyatlas.gla.ac.uk/flyatlas/index.html FlyAtlas2, University of Glasgow, Glasgow, UK]
@@ Line 107: / Line 103: @@
 * <b>Gene Expression Levels by Cell Line</b> (based on modENCODE data):<br />[http://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 />[http://www.ncbi.nlm.nih.gov/geo/info/profiles.html GEO, NCBI, Bethesda, MD USA]
-* <b>modENCODE Tiling Path Expression Search</b> (based on modENCODE data):<br />[https://dgrc.cgb.indiana.edu/cells/TilingSearch DGRC, University of Indiana, Bloomington, IN, USA]
+* <b>GEO Profiles</b>, Gene Expression Omnibus:<br />[http://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 />[http://calla.rnet.missouri.edu/rnaminer/ Cheng Lab, University of Missouri, Mizzou, Columbia, MO, USA]
@@ Line 150: / Line 147: @@
 * <b>COMPLEAT</b>, protein COMPLex Enrichment Analysis Tool:<br />[http://www.flyrnai.org/compleat/ COMPLEAT, DRSC, Harvard Medical School, Boston, MA, USA]
 * <b>DAPPER</b>, database for protein-protein interactions:<br/>[http://dapper.gen.cam.ac.uk/ DAPPER, University of Cambridge, Cambridge, UK]
-* <b>DPiM</b>, Drosophila Protein interaction Map:<br />[https://interfly.med.harvard.edu/ DPiM, Harvard University Medical School, Boston, MA, USA]
+* <b>DPiM</b>, Drosophila Protein interaction Map:<br />Harvard University Medical School, Boston, MA, USA
 * <b>DroID</b>, Drosophila Interactions Database:<br />[http://www.droidb.org/ Drosophila Interaction Database, Detroit, USA]
 * <b>Drosophila PIMRider</b>, Drosophila Protein Interaction Map:<br />[https://pimr.hybrigenics.com/htmlFiles/interactionData/drosophila.html Drosophila PIMRider, Hybrigenics, Paris, France]
@@ Line 161: / Line 158: @@
 * <b>KEGG</b> -- Kyoto Encyclopedia of Genes and Genomes:<br />[http://www.genome.jp/kegg KEGG, Kyoto, Japan]
 * <b>Reactome Pathway Database</b>:<br />[http://www.reactome.org/ Reactome, OICR, Ontario, Canada, EMBL-EBI, UK, NYU Medical Center, NY, USA]
-* <b>SignaLink</b>, A signaling pathway resource with multi-layered regulatory networks:<br />[http://http://signalink.org/ SignaLink, Eötvös Loránd University of Science, Budapest, Hungary]
 * <b>SignedPPI</b>, Searchable Database of Known and Predicted Protein-protein Interactions:<br />[http://www.flyrnai.org/SignedPPI/ DRSC, Harvard Medical School, Boston, MA, USA]
 * <b>STRING</b>, Known and Predicted Protein-Protein Interactions<br />[http://string-db.org/ STRING, SIB, Switzerland CPR, Denmark, and EMBL, Heidelberg, Germany]
@@ Line 174: / Line 170: @@
 * <b>Drosophila App</b>, A mobile application developed by Genesee for use in fly research: <br />[https://itunes.apple.com/us/app/drosophila/id626253408?mt=8 iTunes] | [https://play.google.com/store/apps/details?id=kaver.co.drosophila&hl=en Android]
 * <b>Drosophila Information Service</b>:<br />[http://www.ou.edu/journals/dis/ DIS, Norman, Oklahoma, USA]
+* <b>Drosophilids of the Midwest and Northeast</b>:<br />[https://digitalcommons.mtu.edu/oabooks/1/ by T. Werner, Michigan Technological University and J.Jaenike, University of Rochester]
 * <b>Fly Labs and References</b>, a large list of fly labs and recent publications: <br />[http://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 />[http://www.academictree.org/flytree/ FlyTree, USA]
@@ Line 185: / Line 182: @@
 * <b>Mitotic Spindle Assembly Database</b>:<br />[http://rnai.ucsf.edu/mitospindlescreen/index.html Genes Required for Mitotic Spindle Assembly in S2 cells, University of California, San Francisco, USA]
 * <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>PhenomicDB</b>, A Cross-species Genotype-Phenotype Resource:<br />[http://phenomicdb.de/ Phenotype-Genotype Database, Berlin, Germany]
 * <b>PhospoPep</b> -- phosphorylation site data from ''D. melanogaster'' cell lines:<br />[http://www.phosphopep.org/ The Aebersold group at the ETH in collaboration with the FGCZ in Switzerland, and the ISB, USA.]
 * <b>What's hot today:</b> Current papers in developmental biology and gene function:<br />[http://www.sdbonline.org/sites/fly/aimain/model-organisms-this-week.htm Interactive Fly, Bethesda, MD, USA]
 * <b>The WWW Virtual Library--Drosophila</b>:<br />[http://www.ceolas.org/fly/ Drosophila Virtual Library]
-=ncRNA Databases and Tools=
+=Non-coding (ncRNA) Databases and Tools=
-* <b>DIANA microT-CDS</b>, MicroRNA Target Prediction:<br />[http://diana.imis.athena-innovation.gr/DianaTools/index.php?r=microT_CDS/index DIANA microT-CDS, DIANA LAB, Athens, Greece]
-* <b>DIANA TarBase</b>, MicroRNA Target Database:<br />[http://diana.imis.athena-innovation.gr/DianaTools/index.php?r=tarbase/index DIANA TarBase, DIANA LAB, Athens, Greece]
+==General==
+* <b>NONCODE</b>, An integrated knowledge database dedicated to ncRNAs, especially lncRNAs (last updated 2017):<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 (last updated 2017):<br />[http://rfam.xfam.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 (last updated 2017):<br />[http://rnacentral.org/ RNAcentral, EMBL-EBI, Hinxton, UK]
+==lncRNA==
+* <b>lncrnadb</b>, Long Noncoding RNA Database (last updated 2015):<br />[http://www.lncrnadb.org/ lncrnadb, University of New South Wales, Sydney, Australia]
+* <b>LNCediting</b>, Function of RNA editing in lncRNAs (last updated 2016):<br />[http://bioinfo.life.hust.edu.cn/LNCediting/fly/ LNCediting, Huazhong University of Science and Technology, Wuhan, China and University of Texas, Houston, Texas, USA]
+==miRNA==
+===General===
+* <b>miRBase</b>, A searchable database of published miRNA sequences and annotations (last updated 2014):<br />[http://www.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>Tools4miRs</b>, Manually curated platform gathering methods for the broadly-defined miRNA analysis (last updated 2017):<br />[https://tools4mirs.org/ Tools4miRs, Polish Academy of Sciences and University of Warsaw, Warsaw, Poland]
+* <b>TransmiR</b>, A database of transcription factor-microRNA regulation (last updated 2013):<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 (last updated 2014):<br />[http://diana.imis.athena-innovation.gr/DianaTools/index.php?r=microT_CDS/index DIANA microT-CDS, DIANA LAB, Athens, Greece]
+* <b>MicroCosm Targets</b>, Computationally predicted targets for microRNAs across many species based on MiRanda algorithm (last updated 2007):<br />[http://www.ebi.ac.uk/enright-srv/microcosm/htdocs/targets/v5/ MicroCosm Targets, EMBL-EBI, Hinxton, UK]
+* <b>microRNA.org</b>, Predicted microRNA targets & target downregulation scores based on miRanda and mirSVR algorithms (last updated 2007):<br />[http://www.microrna.org/microrna/home.do microRNA.org, Memorial Sloan-Kettering Cancer Center, New York, NY, USA]
+* <b>MinoTar</b>, Predict microRNA Targets in Coding Sequence (last updated 2010):<br />[http://www.flyrnai.org/cgi-bin/DRSC_MinoTar.pl MinoTar, DRSC, Harvard Medical School, Boston, MA, USA]
+* <b>miRNA - Target Gene Prediction</b> (last updated 2005):<br />[http://www.mirna.embl.de/ miRNA - Target Prediction, EMBL, Heidelberg, Germany]
+* <b>miRNA_Targets</b> (last updated 2011):<br />[http://mamsap.it.deakin.edu.au/~amitkuma/mirna_targetsnew/index.html miRNA targets on full length mRNAs, Deakin University, Victoria, Australia]
+* <b>TargetScanFly</b>, Prediction of microRNA targets based on miRNA seed region and target conservation (last updated 2012):<br />[http://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 2014):<br />[http://diana.imis.athena-innovation.gr/DianaTools/index.php?r=tarbase/index DIANA TarBase, DIANA LAB, Athens, Greece]
+* <b>miRecords</b>, A database of experimentally validated miRNA targets curated from literature (last updated 2009):<br />[http://c1.accurascience.com/miRecords/ miRecords, University of Minnesota, Minneapolis, MN, USA]
+* <b>miRTarBase</b>, Experimentally Validated microRNA-target Interactions Database (last updated 2015):<br />[http://mirtarbase.mbc.nctu.edu.tw/ miRTarBase, ISBLab, Hsinchu, Taiwan]
+* <b>miRTex</b>, A text-mining system that extracts miRNA-gene regulation relations and miRNA-target relations from literature (last updated 2017):<br />[http://research.bioinformatics.udel.edu/miRTex/ miRTex, University of Delaware, Newark, DE, USA]
+===Comparative miRNA Analysis===
+* <b>CoGemiR</b>, Comparative Genomics Analysis of MicroRNA (last updated 2008):<br />[http://cogemir.tigem.it/htdocs/index.html CoGemiR, Telethon Institute of Genetics and Medicine, Naples, Italy]
+* <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]
+* <b>miROrtho</b>, Predictions of precursor miRNA genes covering several animal genomes combining orthology and a Support Vector Machine (last updated 2009):<br />[http://cegg.unige.ch/mirortho miROrtho, University of Geneva, Geneva, Switzerland]
+==rRNA==
+* <b>SILVA</b>, High quality ribosomal RNA databases (last updated 2016):<br />[https://www.arb-silva.de/ SILVA, Max Planck Institute for Marine Microbiology and Jacobs University, Bremen, Germany]
+==tRNA==
 * <b>GtRNAdb</b>, tRNAscan-SE analysis of complete genomes:<br />[http://gtrnadb.ucsc.edu/ GtRNAdb, Lowe lab, University of California, Santa Cruz, Santa Cruz, CA, USA]
-* <b>MinoTar</b>, Predict microRNA Targets in Coding Sequence:<br />[http://www.flyrnai.org/cgi-bin/DRSC_MinoTar.pl MinoTar, DRSC, Harvard Medical School, Boston, MA, USA]
+* <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]
-* <b>miRBase</b>, microRNA data:<br />[http://www.mirbase.org/ 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.
+==snoRNA==
-* <b>miRNA, Target Gene Prediction</b>:<br />[http://www.mirna.embl.de/ miRNA - Target Prediction, EMBL, Heidelberg, Germany]
-* <b>miRNA_Targets</b>:<br />[http://mamsap.it.deakin.edu.au/~amitkuma/mirna_targetsnew/index.html miRNA targets on full length mRNAs, Deakin University, Victoria, Australia]
-* <b>miRTarBase</b>, Experimentally Validated microRNA-target Interactions Database:<br />[http://mirtarbase.mbc.nctu.edu.tw/ miRTarBase, ISBLab, Hsinchu, Taiwan]
-* <b>Rfam</b>, RNA families database of alignments and CMs:<br />[http://www.webcitation.org/getfile?fileid=db1c351a4c279e9cf9697bd2d1962097900701fb Rfam, Wellcome Trust Sanger Institute, Hinxton, UK and Janelia Farm, Ashburn, VA, USA]
-* <b>RNAcentral</b>, provides unified access to the ncRNA sequence data supplied by multiple Expert Databases:<br />[http://rnacentral.org/ RNAcentral, EMBL-EBI, Hingston, UK]
 * <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 ]
-* <b>TargetScanFly</b>, Prediction of microRNA targets:<br />[http://www.targetscan.org/fly_12/ TargetScanFly, Whitehead Institute and MIT Dept. of Biology, USA]]
+==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=
@@ Line 235: / Line 267: @@
 =Phylogenetic Comparison Tools=
-* <b>Assembly/Alignment/Annotation of 12 related ''Drosophila'' species</b>:<br />[http://rana.lbl.gov/drosophila/ Assembly/Alignment/Annotation, LBNL, USA]
 * <b>DIOPT</b>, DRSC Integrative Ortholog Prediction Tool:<br />[http://www.flyrnai.org/cgi-bin/DRSC_orthologs.pl DRSC/TRiP-FGR, Harvard Medical School, Boston, MA, USA]
 * <b>EvoPrinter</b>, Identification of Evolutionarily Resilient DNA Sequences<br />[http://evoprinter.ninds.nih.gov/ NINDS, NIH, Bethesda MD, USA]
@@ Line 241: / Line 272: @@
 * <b>InParanoid</b>, Eukaryotic Ortholog Groups:<br />[http://inparanoid.sbc.su.se/cgi-bin/index.cgi InParanoid, Karolinska Institute, Sweden]
 * <b>MANTiS</b>, a phylogenetic framework for multi-species genome comparisons:<br />[http://www.mantisdb.org/MANTiS/Welcome.html MANTiS, UniversitÃ© Libre de Bruxelles, Belgium]
-* <b>OrthoDB</b>, the Hierarchical Catalog of Orthologs:<br />[http://orthodb.org/orthodb7 OrthoDB, University of Geneva, Switzerland]
+* <b>OrthoDB</b>, the Hierarchical Catalog of Orthologs:<br />[http://www.orthodb.org/ OrthoDB, University of Geneva, Switzerland]
 * <b>flyDIVaS</b>, a comparative genomics database resource of ''Drosophila'' divergence and selection: <br />[http://flydivas.info/ Temple University, Philadelphia, PA, USA]
 * <b>Vista Tools</b> -- Whole Genome Comparative Analysis of the ''D. melanogaster'' (CAF1) Genome:<br />[http://pipeline.lbl.gov/cgi-bin/gateway2?bg=droMel_caf1&selector=vistapoint Whole Genome Comparative Analysis of the D. melanogaster (CAF1) Genome, LBNL, USA]
@@ Line 259: / Line 290: @@
 =Protein Analysis=
 * <b>ExPASy</b>, the SIB Bioinformatics Resource Portal which provides access to scientific databases and software tools in different areas of life sciences:<br />[http://expasy.org/ SIB Swiss Institute of Bioinformatics, Genève, Switzerland]
-* <b>GPCRDB</b>, information system for G protein-coupled receptors (GPCRs):<br />[http://www.gpcr.org/7tm/ GPCRDB, The GPCRDB (G Protein-Coupled Receptor Data Base) partnership]
+* <b>GPCRDB</b>, information system for G protein-coupled receptors (GPCRs):<br />[http://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>MEROPS</b>, an information resource for peptidases:<br />[http://merops.sanger.ac.uk/ MEROPS, Wellcome Trust Sanger Institute, Hinxton, UK]
@@ Line 275: / Line 306: @@
 * <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>Genetic Portraits</b>, An overview of commonly used model organisms in genetic research:<br />[http://highered.mheducation.com/sites/007352526x/student_view0/genetic_portrait_chapters_a-e.html McGraw-Hill Higher Education]
 * <b>Fly on the Wall</b>, a blog by Bethany Christmann regarding fruit flies and research:<br />[http://blogs.brandeis.edu/flyonthewall/ Griffith Lab, Brandeis University, Waltham, MA, USA]
 * <b>FlyMove</b>, an Image, Movie and Interactive Shockwave Resource:<br />[http://flymove.uni-muenster.de/ FlyMove, Muenster, Germany]
@@ Line 304: / Line 334: @@
 * <b>Genie Gene finder for Drosophila</b>:<br />[http://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 /> [http://www.flyrnai.org/hrma HRMA, DRSC, Harvard Medical School, Boston, MA, USA]
-* <b>MEME Suite</b> -- Motif-based Sequence Analysis Tools:<br />[http://meme.nbcr.net/meme/intro.html MEME, U. of Queensland, U. of Washington, USA, UCSD, SDSC, NBCR, CBRC, and National Center for Research Resources]
+* <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 />[http://www.repeatmasker.org/ RepeatMasker Institute for Systems Biology, Seattle, WA, USA]
 * <b>Splice Site Prediction for Drosophila</b>:<br />[http://www.fruitfly.org/seq_tools/splice.html Splice Site Prediction, Berkeley Drosophila Genome Project, University of California, Berkeley, USA]
@@ Line 318: / Line 348: @@
 =Transcription Regulation Databases and Tools=
 * <b>BDTNP</b>, ChIP/chip in vivo DNA binding data:<br />[http://bdtnp.lbl.gov/Fly-Net/chipchip.jsp?w=summary Berkeley Drosophila Transcription Network Project, University of California, Berkeley, USA]
-* <b>cis-analyst</b>, Searching the Drosophila genome for clusters of binding sites: <br />[http://rana.lbl.gov/cis-analyst/ cis-analyst, Berkeley, USA]
 * <b>CORE</b>, A database utilizing the ElemeNT algorithm (see below) to annotate individual Drosophila observed TSS (using either CAGE or RNAseq data) for the presence of the various core promoter elements: <br />[http://lifefaculty.biu.ac.il/gershon-tamar/index.php/core-description Juven-Gershon Lab, Bar-Ilan University, Ramat-Gan, Israel]
 * <b>DBD</b>, Transcription factor prediction database: <br />[http://www.transcriptionfactor.org/index.cgi?Home DBD, MRC, Cambridge, UK]
@@ Line 329: / Line 358: @@
 * <b>Neural Network Promoter Prediction for Drosophila</b>:<br />[http://www.fruitfly.org/seq_tools/promoter.html Neural Network Promoter Prediction, Berkeley Drosophila Genome Project, University of California, Berkeley, 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, USA]
-* <b>PREdictor</b>, to identify Polycomb/Trithorax response elements: <br />[http://bibiserv.techfak.uni-bielefeld.de/predictor/ PREdictor, Bielefeld University, Germany]
 * <b>REDfly</b>, Regulatory Element Database for Drosophila:<br />[http://redfly.ccr.buffalo.edu/ REDfly, University at Buffalo, New York, USA]
 * <b>The Drosophila Transcription Factor Database</b>:<br />[http://www.flytf.org/ FlyTF.org, MRC Cambridge, UK]

Difference between revisions of "FlyBase:Drosophila Online Resources"

Revision as of 17:55, 25 July 2018

Contents

Atlases, Images and Videos

CRISPRs and TALENs

Data Repositories

Drosophila Genomes Data and Metadata

Gene Expression Databases and Tools

Gene Groups

General Bioinformatics Tools

Genome Sequencing Projects

Human Disease: Drosophila Models and Orthologous Genes

Interaction and Pathway Databases

Laboratory Resources

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

Public Education

RNAi

Sequence Analysis

Taxonomy

Transcription Regulation Databases and Tools

Suggest a tool or resource

Navigation menu

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