Difference between revisions of "FlyBase:Resources"

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=Model Organisms=
 
{| class="wikitable" border="1"
 
|-
 
! Database
 
! Organism
 
! Organism (Genus and species)
 
|-
 
| [http://hymenopteragenome.org/beebase/ BeeBase]
 
| Honey Bee
 
| Apis mellifera
 
|-
 
| [http://beetlebase.org/ BeetleBase]
 
| Red Flour Beetle
 
| Tribolium castaneum
 
|-
 
| [http://dictybase.org/ DictyBase]
 
| Soil Amoeba
 
| Dictyostelium discoideum
 
|-
 
| [http://ecocyc.org/ EcoCyc]
 
| Bacteria
 
| Escherichia coli
 
|-
 
| [http://www.gramene.org/ Gramene]
 
| Grasses
 
|
 
|-
 
| [http://www.informatics.jax.org/ MGI]
 
| Mouse
 
| Mus musculus
 
|-
 
| [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=OMIM/ OMIM]
 
| Human
 
| Homo sapiens
 
|-
 
| [http://www.yeastgenome.org// SGD]
 
| Budding Yeast
 
| Saccharomyces cerevisiae
 
|-
 
| [http://www.genedb.org/genedb/pombe/index.jsp S. pombe GeneDB]
 
| Fission Yeast
 
| Schizosaccharomyces pombe
 
|-
 
| [http://www.arabidopsis.org/ TAIR]
 
| Mouse-ear cress
 
| Arabidopsis thaliana
 
|-
 
| [http://www.vectorbase.org/index.php VectorBase]
 
| Mosquitos and Deer Tick
 
| Anopheles gambiae, Aedes aegypti, Culex pipiens quinquefasciatus, Ixodes scapularis
 
|-
 
| [http://www.wormbase.org/ WormBase]
 
| Round worms
 
| Caenorhabditis
 
|-
 
| [http://zfin.org/cgi-bin/webdriver?MIval=aa-ZDB_home.apg ZFIN]
 
| Zebrafish
 
| Danio rerio
 
|}
 
  
=Related Projects=
 
:[http://www.gmod.org/ GMOD]
 
:[http://www.geneontology.org/ Gene Ontology (GO)]
 
:[http://www.genomeknowledge.org/ Reactome]
 
:[http://www.fruitfly.org/ BDGP (Berkeley Drosophila Genome Project)]
 
:[http://dgrc.cgb.indiana.edu/ DGRC (Drosophila Genomics Resource Center)]
 
:[http://www.ou.edu/journals/dis/byissue.html DIS by issue]
 
:[http://www.flyexpress.net/ FlyExpress]
 
:[http://www.sdbonline.org/fly/aimain/1aahome.htm Interactive Fly]
 
:[http://www.modencode.org/ modENCODE]
 
:[http://www.textpresso.org/fly/ Textpresso for Fly]
 
 
=Stock Collections=
 
===''D. melanogaster'' Collections===
 
:[http://flystocks.bio.indiana.edu/ Bloomington]
 
:[http://www.drosdel.org.uk/ DrosDel]
 
:[http://drosophila.med.harvard.edu/ Exelixis (Harvard)]
 
:[http://flypush.imgen.bcm.tmc.edu/pscreen/ GDP (Baylor)]
 
:[http://www.dgrc.kit.ac.jp/ Kyoto]
 
:[http://www.shigen.nig.ac.jp/fly/nigfly/ NIG-Fly]
 
:[http://stockcenter.vdrc.at/control/main VDRC]
 
 
===Species Collections===
 
:[http://kyotofly.kit.jp/cgi-bin/ehime/index.cgi Ehime]
 
:[https://stockcenter.ucsd.edu/info/welcome.php 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==
 
 
 
[[Category:Public Resources]]
 

Latest revision as of 17:34, 13 February 2014