FlyBase:Drosophila Online Resources

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
• Electron micrograph maps of D. 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
• FlyGut, An interactive Database that aims to provide a comprehensive atlas of the Drosophila melanogaster adult midgut (see also, FlyGut-seq):
  Buchon Lab, Cornell University, Ithaca, NY, USA & Lemaitre Lab, EPFL, Lausanne, Switzerland
• 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 describing marker phenotypes in the fruit fly:
  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
• 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

CRISPRs and TALENs

• Cas9 Design:
  Center for Bioinformatics, Peking University, Peking, China
• 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, Harvard Medical School, Boston, MA, USA
• DRSC Finding CRISPRs, Drosophila CRISPR gRNA design search tool:
  DRSC, 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
• TAL Effectors:
  Zhang lab, MIT, 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
• 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
• NCBI Map Viewer, A genome view of Drosophila melanogaster:
  NCBI, Bethesda, MD USA
• PubMed, Biomedical literature full-text archive:
  PubMed, NCBI, Bethesda, MD USA
• PubMed Central, Biomedical literature citations and abstracts:
  PubMed Central, 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

• 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. ananassae Genome:
  D. ananassae Organism Overview, NCBI, USA
  D. ananassae Genome Assembly Report, NCBI, USA
  D. ananassae 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. 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. 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. 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
• cisPatterns, A database of over 100 Drosophila GAL4-driver lines regulated by single cis-regulatory enhancers:
  Jermaine Ross and the Odenwald Lab, NINDS, NIH, Bethesda MD, USA
• DGRC, Cell Line Expression tool (based on modENCODE data):
  DGRC, University of Indiana, Bloomington, IN, USA
• DRSC, Cell Line Expression tool (based on modENCODE data):
  DRSC, Harvard Medical School, Boston, MA, USA
• 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
• 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
• RNAMiner, A Bioinformatics Protocol for Mining Large RNA-Seq Transcriptomics Data:
  Cheng Lab, University of Missouri, Mizzou, Columbia, MO, USA

Gene Groups

• GLAD, an Online Database of Gene List Annotations for Drosophila:
  DRSC, 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
• Cytoscape -- Network Data Integration, Analysis, and Visualization in a Box:
  Cytoscape, Cytoscape Consortium, Canada, France, and USA
• DAVID (NIH) -- Database for Annotation , Visualization and Integrated Discovery:
  DAVID, NIH, Bethesda, MD, 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, 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, Harvard Medical School, Boston, MA, USA

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:
  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
• FlyCyc -- Curated Drosophila melanogaster Pathways:
  FlyCyc, Harvard University, Cambridge, USA
• FlyNet Gene Prioritization:
  NetBioLab, Yonsei University, Seoul, Korea
• 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
• SignaLink, A signaling pathway resource with multi-layered regulatory networks:
  SignaLink, Eötvös Loránd University of Science, Budapest, Hungary
• 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
• 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
• PhenomicDB, A Cross-species Genotype-Phenotype Resource:
  Phenotype-Genotype Database, Berlin, Germany
• 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

ncRNA Databases and Tools

• DIANA microT-CDS, MicroRNA Target Prediction:
  DIANA microT-CDS, DIANA LAB, Athens, Greece
• DIANA TarBase, MicroRNA Target Database:
  DIANA TarBase, DIANA LAB, Athens, Greece
• GtRNAdb, tRNAscan-SE analysis of complete genomes:
  GtRNAdb, Lowe lab, University of California, Santa Cruz, Santa Cruz, CA, USA
• MinoTar, Predict microRNA Targets in Coding Sequence:
  MinoTar, DRSC, Harvard Medical School, Boston, MA, USA
• miRBase, microRNA data:
  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.

• miRNA, Target Gene Prediction:
  miRNA - Target Prediction, EMBL, Heidelberg, Germany
• miRNA_Targets:
  miRNA targets on full length mRNAs, Deakin University, Victoria, Australia
• miRTarBase, Experimentally Validated microRNA-target Interactions Database:
  miRTarBase, ISBLab, Hsinchu, Taiwan
• Rfam, RNA families database of alignments and CMs:
  Rfam, Wellcome Trust Sanger Institute, Hinxton, UK and Janelia Farm, Ashburn, VA, USA
• RNAcentral, provides unified access to the ncRNA sequence data supplied by multiple Expert Databases:
  RNAcentral, EMBL-EBI, Hingston, UK
• snOPY, a snoRNA orthological gene database providing comprehensive information about snoRNAs, snoRNA gene loci and target RNAs.:
  snOPY, University of Miyazaki, Japan
• TargetScanFly, Prediction of microRNA targets:
  TargetScanFly, Whitehead Institute and MIT Dept. of Biology, 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, Harvard Medical School, Boston, MA, USA
• DIOPT-DIST: DIOPT Diseases and Traits, DRSC Disease Gene Query Tool:
  DRSC, 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
• 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

• 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 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 Polymorphism Database:
  DGRP2, 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
• FlyVar Project: A Database of Drosophila Genetics Variations
  FlyVar, Fudan University, Shanghai, China and Baylor College of Medicine, Houston, TX, 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
• 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
• 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
• 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
• Genetic Portraits, An overview of commonly used model organisms in genetic research:
  McGraw-Hill Higher Education
• 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, Drosophila RNAi Screening Center:
  DRSC, Harvard Medical School, Boston, MA, USA
• Search by gene(s) to find hits in DRSC screens:
  DRSC, 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, 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, Harvard Medical School, Boston, MA, USA
• Predicted Off-Target Free Sequence Regions:
  DRSC, 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, Harvard Medical School, Boston, MA, USA
• SnapDragon, RNAi Design:
  DRSC, Harvard Medical School, Boston, MA, USA
• TRiP, Transgenic RNAi Project:
  Transgenic RNAi Project, DRSC, 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, 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
• cis-analyst, Searching the Drosophila genome for clusters of binding sites:
  cis-analyst, 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
• FlyReg, 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
• 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
• 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

Suggest a tool or resource

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