Difference between revisions of "FlyBase:Resources"

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=Listing of all resources=
 
=Listing of all resources=
−
===Drosophila Network 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
  
 
===Drosophila Material Resources===
 
===Drosophila Material Resources===

Revision as of 20:39, 23 May 2013

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

Bloomington
DrosDel
Exelixis (Harvard)
GDP (Baylor)
Kyoto
NIG-Fly
VDRC

Species Collections

Ehime
UC San Diego

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

Drosophila Material Resources

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