FlyBase:Drosophila Online Resources

Atlases, Images and Videos

• BDTNP, A cellular resolution 3D gene expression and morphology Atlas of the blastoderm.
  Berkeley Drosophila Transcription Network Project, University of California, Berkeley, USA
• CSIRO Anatomical Atlas of Flies:
  CSIRO Entomology, Australia
• Electron micrograph maps of Drosophila melanogaster polytene chromosomes:
  Sorsa Maps, Helsinki, Finland
• FlyBrain, an Online Atlas and Database of the Drosophila Nervous System:
  FlyBrain, University of Arizona, Tucson, USA
• 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, National Institute of Basic Biology, Okazaki, Japan
• Jove, videos of experimental techniques:
  Jove, Journal of Visualized Experiments, USA
• Scans of Bridges' original 1935 polytene drawings for D. melanogaster:
  GEM Website, University of Hawaii, 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

Data Repositories

• Array Express - Functional Genomics Data:
  EMBL-EBI, Cambridge, 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, Cambridge, UK
• Ensembl Genome Browser:
  EMBL-EBI, Hinxton, UK
• GenBank,the NIH genetic sequence database:
  GenBank, NCBI, Bethesda, MD USA
• GEO Datasets, Gene Expression Omnibus:
  NCBI, Bethesda, MD USA
• NCBI, National Center fo Biotechnology Information:
  Bethesda, MD USA
• PubMed, Biomedical literature full-text archive:
  PubMed, NCBI, Bethesda, MD USA
• PubMed Central, Biomedical literature citations and abstracts:
  PubMed, NCBI, Bethesda, MD USA
• SRA, Sequence Read Archive:
  SRA, NCBI, Bethesda, MD, USA
• UCSC Genome Browser Gateway - D. melanogaster:
  UCSC Genome Browser, UC Santa Cruz, USA

Data and Metadata for Drosophila Genomes

• D. albomicans Genome:
  D. albomicans Organism Overview, NCBI, USA
  D. albomicans Genome Assembly Report, ENA, UK
• D. ananassae Genome:
  D. ananassae Organism Overview, NCBI, USA
  D. ananassae 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. 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. 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. 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

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

Gene Expression Databases and Tools

• BDGP in situ, Patterns of gene expression in Drosophila embryogenesis:
  Gene expression database, BDGP, UC 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
• FlAnnotator, Annotation of Gene Expression:
  FlyAnnotator
• FlyEx, a Database of Segmentation Gene Expression in Drosophila:
  FlyEx, St. Petersburg State Polytechnical University, Russia
  FlyEx, Stony Brook University, USA
• FlyExpress, an Expression Pattern Search Engine:
  FlyExpress, Arizona State University, USA
• FlyLight, Expression Patterns of GAL4 Driver Lines:
  HHMI, Janelia Farms Research Campus
• flytrap, a database of P{GAL4} enhancer traps and their expression in brains:
  flytrap, University of Edinburgh, UK
• GEO Profiles, Gene Expression Omnibus:
  GEO, NCBI, Bethesda, MD 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
• Cytoscape - Network Data Integration, Analysis, and Visualization in a Box:
  Cytoscape
• DAVID (NIH) - Database for Annotation , Visualization and Integrated Discovery:
  DAVID, NIH, Bethesda, MD, USA
• FlyMine, an integrated database for Drosophila &amp: Anopheles genomics:
  University of Cambridge, United Kingdom
• 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
• GOrilla - Gene Ontology enRIchment and anaLysis and viuaLizAtion tool:
  GOrilla, Israel

Interaction and Pathway Databases

• BioGRID, The General Repository for Interaction Datasets:
  BioGRID, Mount Sinai Hospital, Toronto, Canada
• DPiM, Drosophila Protein interaction Map:
  DPiM, 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
• 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
• STRING, Known and Predicted Protein-Protein Interactions
  STRING, SIB, Switzerland CPR, Denmark, and EMBL, UK

Miscellaneous

• Bloomington Stock Center, Drosophila and Human Disease page:
  Bloomington Stock Center, Bloomington, IN, USA
• Drosophila Information Service:
  DIS, Norman, Oklahoma, USA
• FlyTree, the Drosophila Researcher Genealogy has been incorporated into the Academic Tree Project:
  FlyTree, USA
• GenAge - The ageing Gene Database:
  GeneAge
• Homophila, Human Disease to Drosophila Gene Database:
  Homophila, San Diego, 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
• 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
• 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.
• The WWW Virtual Library--Drosophila:
  Drosophila Virtual Library

Phylogenetic Comparison Tools

• Assembly/Alignment/Annotation of 12 related Drosophila species:
  Assembly/Alignment/Annotation, LBNL, USA
• DIOPT, DRSC Integrative Ortholog Prediction Tool:
  DRSC, Harvard Medical School, Boston, MA, USA
• EvoPrinter, Identification of Evolutionarily Resilient DNA Sequences
  NINDS, NIH, Bethesda MD, USA
• InParanoid, Eukaryotic Ortholog Groups:
  InParanoid, Karolinska Institute, Sweden
• MANTiS a phylogenetic framework for multi-species genome comparisons:
  MANTiS, Université Libre de Bruxelles, Belgium
• NCBI HomoloGene - automated system fo constructing putative homology groups:
  NCBI, Bethesda, MA, USA
• OrthoDB, the Hierarchical Catalog of Orthologs:
  http://orthodb.org/orthodb7 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 Polymorphism Database:
  Drosophila Polymorphism Database, Univ. Autònoma de 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

Protein Analysis

• 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
• Panther protein classification system:
  Panther Protein Classification System, Applied Biosystems & Celera, USA
• PDB, Protein Data Bank:
  PDB, The Research Collaboratory for Structural Bioinformatics (RCSB) consortium
• SMART, Simple Modular Architecture Research Tool:
  SMART, Protein Domain Analysis, EMBL, Heidleberg
• UniProtKB, a comprehensive catalog of information on proteins:
  UniProtKB, The UniProt Consortium

RNA and RNAi Databases and Tools

• DRSC, Drosophila RNAi Screening Center:
  DRSC, Harvard Medical School, Boston, MA, USA
• GenomeRNAi, Heidelberg, a database of RNA interference (RNAi) screens in cultured Drosophila cells:
  GenomeRNAi, DKFZ, Heidelberg, Germany
• miRBase, microRNA data:
  miRBase, University of Manchester, UK
• miRNA, Target Gene Prediction:
  miRNA - Target Prediction, EMBL, Heidelberg, Germany
• miRNA_Targets:
  miRNA targets on full length mRNAs, Deakin University, Victoria, Australia
• Rfam, RNA families database of alignments and CMs:
  Rfam, Wellcome Trust Sanger Institute, Hinxton, UK and Janelia Farm, Ashburn, VA, USA
• TargetScanFly, Prediction of microRNA targets:
  TargetScanFly, Whitehead Institute and MIT Dept. of Biology, USA
• UP-TORR Fly, a tool for identifying updated targets of RNAi reagents:
  Updated Targets of RNAi Reagents, DRSC, Harvard Medical School, Boston, MA,USA

Sequence Analysis

• 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
• 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

• BDTNP, ChIP/chip in vivo DNA binding data:
  Berkeley Drosophila Transcription Network Project, University of California, Berkeley, USA
• cis-analyst, to search the Drosophila genome for clusters of binding sites:
  cis-analyst, Berkeley, USA
• DBD: Transcription factor prediction database:
  DBD, MRC, Cambridge, UK
• DNase I Footprint Database::
  University of Manchester Bioinformatics Resources, University of Manchester, UK
• 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
• OnTheFly, Database of Drosophila Transcription Factors and Transcription Factor Binding Sites
  OnTheFly, Columbia University, USA
• Neural Network Promoter Prediction for Drosophila:
  Neural Network Promoter Prediction, Berkeley Drosophila Genome Project, University of California, Berkeley, USA
• PREdictor, to identify Polycomb/Trithorax response elements:
  PREdictor, Bielefeld University, Germany
• 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