FlyBase:Drosophila Online Resources
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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 - FlyGut, an atlas of the Drosophila adult midgut :
Buchon Lab, Cornell University, Ithaca, NY, USA - FlyMove, an Image, Movie and Interactive Shockwave Resource:
FlyMove, Muenster, Germany - FlyPNS, D. melanogaster embryonic and larval peripheral nervous system:
FlyPNS, CNRS, Institut Jacques Monod, 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 - Dynamic Atlas of Drosophila development - A morphodynamic atlas from Lefebvre et al., 2025 that unifies fixed and live datasets (including gene expression profiles) into a single, morphological consensus timeline:
University of California Santa Barbara, Santa Barbara, California
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 - 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 - 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 - 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, ENA, UK - D. americana Genome:
D. americana Organism Overview, NCBI, USA
D. americana Genome Assembly Report, ENA, UK - D. ananassae Genome:
D. ananassae Organism Overview, NCBI, USA
D. ananassae Genome Assembly Report, ENA, UK - D. arizonae Genome:
D. arizonae Organism Overview, NCBI, USA
D. arizonae Genome Assembly Report, ENA, UK - D. biarmipes Genome:
D. biarmipes Organism Overview, NCBI, USA
D. biarmipes Genome Assembly Report, ENA, UK - D. bipectinata Genome:
D. bipectinata Organism Overview, NCBI, USA
D. bipectinata Genome Assembly Report, ENA, UK - D. busckii Genome:
D. busckii Organism Overview, NCBI, USA
D. busckii Genome Assembly Report, ENA, UK - D. erecta Genome:
D. erecta Organism Overview, NCBI, USA
D. erecta Genome Assembly Report, ENA, UK - D. elegans Genome:
D. elegans Organism Overview, NCBI, USA
D. elegans Genome Assembly Report, ENA, UK - D. eugracilis Genome:
D. eugracilis Organism Overview, NCBI, USA
D. eugracilis Genome Assembly Report, ENA, UK - D. ficusphila Genome:
D. ficusphila Organism Overview, NCBI, USA
D. ficusphila Genome Assembly Report, ENA, UK - D. grimshawi Genome:
D. grimshawi Organism Overview, NCBI, USA
D. grimshawi Genome Assembly Report, ENA, UK - D. kikkawai Genome:
D. kikkawai Organism Overview, NCBI, USA
D. kikkawai Genome Assembly Report, ENA, UK - D. melanogaster Genome:
D. melanogaster Organism Overview, NCBI, USA
D. melanogaster Genome Assembly Report, ENA, UK - D. miranda Genome:
D. miranda Organism Overview, NCBI, USA
D. miranda Genome Assembly Report, ENA, UK - D. mojavensis Genome:
D. mojavensis Organism Overview, NCBI, USA
D. mojavensis Genome Assembly Report, ENA, UK - D. navojoa Genome:
D. navojoa Organism Overview, NCBI, USA
D. navojoa Genome Assembly Report, ENA, UK - D. persimilis Genome:
D. persimilis Organism Overview, NCBI, USA
D. persimilis Genome Assembly Report, ENA, UK - D. pseudoobscura Genome:
D. pseudoobscura Organism Overview, NCBI, USA
D. pseudoobscura Genome Assembly Report, ENA, UK - D. rhopaloa Genome:
D. rhopaloa Organism Overview, NCBI, USA
D. rhopaloa Genome Assembly Report, ENA, UK - D. sechellia Genome:
D. sechellia Organism Overview, NCBI, USA
D. sechellia Genome Assembly Report, ENA, UK - D. simulans Genome:
D. simulans Organism Overview, NCBI, USA
D. simulans Genome Assembly Report, ENA, UK - D. suzukii Genome:
D. suzukii Organism Overview, 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, ENA, UK - D. virilis Genome:
D. virilis Organism Overview, NCBI, USA
D. virilis Genome Assembly Report, ENA, UK - D. willistoni Genome:
D. willistoni Organism Overview, NCBI, USA
D. willistoni Genome Assembly Report, ENA, UK - D. yakuba Genome:
D. yakuba Organism Overview, 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, an atlas of the Drosophila adult midgut :
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
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 - 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 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 - 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
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
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 - 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 - 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 - 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, Université 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 - 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, 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.