FlyBase:Resources
Revision as of 20:39, 23 May 2013 by Susan St.Pierre (talk | contribs) (→Drosophila Material Resources)
Model Organisms
| Database | Organism | Organism (Genus and species) |
|---|---|---|
| BeeBase | Honey Bee | Apis mellifera |
| BeetleBase | Red Flour Beetle | Tribolium castaneum |
| DictyBase | Soil Amoeba | Dictyostelium discoideum |
| EcoCyc | Bacteria | Escherichia coli |
| Gramene | Grasses | |
| MGI | Mouse | Mus musculus |
| OMIM | Human | Homo sapiens |
| SGD | Budding Yeast | Saccharomyces cerevisiae |
| S. pombe GeneDB | Fission Yeast | Schizosaccharomyces pombe |
| TAIR | Mouse-ear cress | Arabidopsis thaliana |
| VectorBase | Mosquitos and Deer Tick | Anopheles gambiae, Aedes aegypti, Culex pipiens quinquefasciatus, Ixodes scapularis |
| WormBase | Round worms | Caenorhabditis |
| ZFIN | Zebrafish | Danio rerio |
Related Projects
- GMOD
- Gene Ontology (GO)
- Reactome
- BDGP (Berkeley Drosophila Genome Project)
- DGRC (Drosophila Genomics Resource Center)
- DIS by issue
- FlyExpress
- Interactive Fly
- modENCODE
- Textpresso for Fly
Stock Collections
D. melanogaster Collections
Species Collections
Other public collections
- Drosophila Gene Search Project
- Information about ordering P{GS} lines can be found at http://gsdb.biol.metro-u.ac.jp/~dclust/index.html
- Ehime Drosophila Species Stock Center of Japan
- A collection of wild-type strains of D. melanogaster and strains of some 30 species can be found at http://kyotofly.kit.ac.jp/ehime/
- FlyTrap Stock Collection
- GFP protein trap lines from the FlyTrap project can be obtained at Yale University, USA at http://flytrap.med.yale.edu/
- FlyView Stock Collection
- Enhancer trap lines from the FlyView project can be obtained at University of Muenster, Germany at http://flyview.uni-muenster.de/
- Kyorin-Fly
- A collection of mutant and wildtype stocks of Drosophila species, especially the Drosophila ananassae species subgroup, D. auraria complex, and D. hydei. http://kyotofly.kit.jp/cgi-bin/kyorin/index.cgi
- Tübingen Drosophila Stock Collection
- A list of approximately 2,000 Drosophila stocks at the Max-Planck-Institute for Developmental Biology.
- UC San Diego Drosophila Stock Center
- Approximately 270 different Drosophila species at University of San Diego, USA can be obtained at https://stockcenter.ucsd.edu/info/welcome.php
- University of Cambridge FlyProt project
- Annotations, expression patterns and sequence data for the YFP protein trap lines from the FlyProt project can be viewed on the Flannotator at http://www.flyprot.org. Stocks are available from the Kyoto Stock Center.
Vectors and Constructs
http://flybase.org/static_pages/lists/vectors.html
Listing of all resources
Drosophila Network Resources
Comparative Analyses and Genome Databases
Assembly/Alignment/Annotation of 12 related Drosophila species: »Assembly/Alignment/Annotation, LBNL, USA BDGP Single Nucleotide Polymorphism (SNP) Project: »Berkeley Drosophila Genome Project, University of California, Berkeley, USA Berkeley Drosophila Genome Project (BDGP): »BDGP, University of California, Berkeley, USA BDTNP, ChIP/chip in vivo DNA binding data: »Berkeley Drosophila Transcription Network Project, University of California, Berkeley, USA CluSTr protein sequence similarity analysis of Drosophila: »CluSTr proteome analysis, EBI, UK D. pseudoobscura genome project: »Human Genome Sequencing Center, Baylor College of Medicine, USA D. simulans genome project: »Genome Sequencing Center, Washington University, USA D. yakuba genome project: »Genome Sequencing Center, Washington University, USA D.melanogaster UCSC Genome Browser Gateway: »University of California, Santa Cruz, USA DDBJ, the DNA Data Bank of Japan: »DDBJ, National Institute of Genetics, Mishima, Japan DNase I Footprint Database: »University of Manchester Bioinformatics Resources, University of Manchester, UK Drosophila Heterochromatin Genome Project (DHGP): »DHGP, Lawrence Berkeley National Laboratory, USA Drosophila melanogaster Exon Database (DEDB): »DEDB, National University of Singapore Drosophila Polymorphism Database: »Drosophila Polymorphism Database, Univ. Autònoma de Barcelona, Spain Drosophila Population Genomic Project (DPGP): »DPGP, University of California, Davis, USA Drosophila simulans and yakuba sequencing projects: »DPGP, University of California, Davis, USA Drosophilidae Taxonomic Database: »Drosophilidae Taxonomic Database, Japan Drosophilidae Taxonomy - Collection of Papers: »Japan Drosophila Database (JDD) on Taxonomy, Japan DRSC, Drosophila RNAi Screening Center: »DRSC, Harvard Medical School, Boston, MA, USA EMBL Nucleotide Sequence Database: »EMBL Nucleotide Sequence Database, EBI, Cambridge, UK EPD, the Eukaryotic Promoter Database: »EPD, Epalinges s/Lausanne, Switzerland euGenes, Genomic Information for Eukaryotic Organisms, including Drosophila: » euGenes, Indiana University, USA EvoPrinter, Identification of Evolutionarily Resilient DNA Sequences »NINDS, NIH, Bethesda MD, USA FLIGHT, Fly database for the Integration of Genomic and High-Throughput data: »FLIGHT Database, Ludwig Institute for Cancer Research, London, UK FlyAtlas, the Drosophila adult gene expression atlas: »FlyAtlas, University of Glasgow, UK FlyMine, an integrated database for Drosophila & Anopheles genomics: »University of Cambridge, United Kingdom FlyPhenomics, phenotypic differences between species of the D. melanogaster subgroup: »FlyPhenomics, Paris, France FlySNP Project: »FlySNP, Austrian Academy of Sciences, Austria GenBank,the NIH genetic sequence database: »GenBank, NCBI, Bethesda, MD USA GenomeRNAi, Heidelberg, a database of RNA interference (RNAi) screens in cultured Drosophila cells: »GenomeRNAi, DKFZ, Heidelberg, Germany GEO, NCBI's Gene Expression Omnibus: »GEO, NCBI, Bethesda, MD USA GPCRDB, information system for G protein-coupled receptors (GPCRs): »GPCRDB, The GPCRDB (G Protein-Coupled Receptor Data Base) partnership Homophila, Human Disease to Drosophila Gene Database: » Homophila, San Diego, USA InParanoid, Eukaryotic Ortholog Groups: »InParanoid, Karolinska Institute, Sweden InterPro protein domain analysis of Drosophila: »InterPro proteome analysis, EBI, UK MANTiS a phylogenetic framework for multi-species genome comparisons: »MANTiS, Université Libre de Bruxelles, Belgium MEROPS, an information resource for peptidases: »MEROPS, The Sanger Institute, Cambridge, UK miRBase, microRNA data: »miRBase, The Sanger Institute, Cambridge, UK miRNA, Target Gene Prediction: »miRNA - Target Prediction, EMBL, Heidelberg, Germany 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 NHGRI Drosophila Genome Sequencing Proposals, Status of Sequencing: »National Human Genome Research Institute, Bethesda, MD, USA 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 - 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. Proteome analysis of Drosophila: »Proteome analysis, EBI, UK PubMed, Biomedical literature citations and abstracts: »PubMed, NCBI, Bethesda, MD USA REDfly, Regulatory Element Database for Drosophila: »REDfly, University at Buffalo, New York, USA Rfam, RNA families database of alignments and CMs: »Rfam, the Sanger Institute, Cambridge, UK and Janelia Farm, Ashburn, VA, USA Sebida, Sex Bias Database: »Sebida, MPI Martinsried, Germany TaxoDros, the database on Taxonomy of Drosophilidae: »TaxoDros, University of Zurich, Switzerland The Drosophila Transcription Factor Database: »FlyTF.org, MRC Cambridge, UK The McGill Drosophila melanogaster Genome Project: »McGill Drosophila Genome Project, Canada TRANSFAC, A database of transcription factors and their binding sites: »TRANSFAC, Braunschweig, Germany TransTerm, a Translational Signal Database: »TransTerm, Dunedin, New Zealand UniProtKB, a comprehensive catalog of information on proteins: »UniProtKB, The UniProt Consortium Whole genome comparative analysis of D. melanogaster and D. pseudoobscura: »Whole genome analysis, LBNL, USA