Difference between revisions of "FlyBase:Drosophila Online Resources"

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* BDGP Single Nucleotide Polymorphism (SNP) Project:<br />[http://www.fruitfly.org/SNP/ Berkeley Drosophila Genome Project, University of California, Berkeley, USA]
 
* BDGP Single Nucleotide Polymorphism (SNP) Project:<br />[http://www.fruitfly.org/SNP/ Berkeley Drosophila Genome Project, University of California, Berkeley, USA]
 
* Berkeley Drosophila Genome Project (BDGP):<br />[http://www.fruitfly.org/ BDGP, University of California, Berkeley, USA]
 
* Berkeley Drosophila Genome Project (BDGP):<br />[http://www.fruitfly.org/ BDGP, University of California, Berkeley, USA]
* Bioconductor, Open Source Software for Bioinformatics<br />[http://www.bioconductor.org/ Fred Hutchinson Cancer Research Center, Seattle, USA]
+
* BDTNP, ChIP/chip in vivo DNA binding data:<br />[http://bdtnp.lbl.gov/Fly-Net/chipchip.jsp?w=summary Berkeley Drosophila Transcription Network Project, University of California, Berkeley, USA]
 +
* Bioconductor:<br />[http://www.bioconductor.org/ Fred Hutchinson Cancer Research Center, Seattle, USA]
 
* CluSTr protein sequence similarity analysis of Drosophila:<br />[http://www.ebi.ac.uk/integr8/ClustrAnalysisPage.do?orgProteomeID=17 CluSTr proteome analysis, EBI, UK]
 
* CluSTr protein sequence similarity analysis of Drosophila:<br />[http://www.ebi.ac.uk/integr8/ClustrAnalysisPage.do?orgProteomeID=17 CluSTr proteome analysis, EBI, UK]
 
* ''D. pseudoobscura'' genome project:<br />[https://www.hgsc.bcm.edu/arthropods/drosophila-pseudoobscura-genome-project D. pseudoobscura Human Genome Sequencing Center, Baylor College of Medicine, USA]
 
* ''D. pseudoobscura'' genome project:<br />[https://www.hgsc.bcm.edu/arthropods/drosophila-pseudoobscura-genome-project D. pseudoobscura Human Genome Sequencing Center, Baylor College of Medicine, USA]
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* ''D. melanogaster'' UCSC Genome Browser Gateway:<br />[http://genome.ucsc.edu/cgi-bin/hgGateway?hgsid=392011865_gtu3Ax0AafEkl925NpQE4ZH8Py7I&clade=insect&org=0&db=0 D. melanogaster, UCSC Genome Browser, University of California, Santa Cruz, USA]
 
* ''D. melanogaster'' UCSC Genome Browser Gateway:<br />[http://genome.ucsc.edu/cgi-bin/hgGateway?hgsid=392011865_gtu3Ax0AafEkl925NpQE4ZH8Py7I&clade=insect&org=0&db=0 D. melanogaster, UCSC Genome Browser, University of California, Santa Cruz, USA]
 
* DDBJ, the DNA Data Bank of Japan:<br />[http://www.ddbj.nig.ac.jp/ DDBJ, National Institute of Genetics, Mishima, Japan]
 
* DDBJ, the DNA Data Bank of Japan:<br />[http://www.ddbj.nig.ac.jp/ DDBJ, National Institute of Genetics, Mishima, Japan]
 +
* DNase I Footprint Database<nowiki>: </nowiki><br />[http://www.flyreg.org/ University of Manchester Bioinformatics Resources, University of Manchester, UK]
 
* ''Drosophila melanogaster'' Exon Database (DEDB):<br />[http://proline.bic.nus.edu.sg/dedb/ DEDB, National University of Singapore]
 
* ''Drosophila melanogaster'' Exon Database (DEDB):<br />[http://proline.bic.nus.edu.sg/dedb/ DEDB, National University of Singapore]
 
* Drosophila Polymorphism Database:<br />[http://bioinformatica.uab.es/dpdb/ Drosophila Polymorphism Database, Univ. Autònoma de Barcelona, Spain]
 
* Drosophila Polymorphism Database:<br />[http://bioinformatica.uab.es/dpdb/ Drosophila Polymorphism Database, Univ. Autònoma de Barcelona, Spain]
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* DRSC, Drosophila RNAi Screening Center:<br />[http://www.flyrnai.org/index.html DRSC, Harvard Medical School, Boston, MA, USA]
 
* DRSC, Drosophila RNAi Screening Center:<br />[http://www.flyrnai.org/index.html DRSC, Harvard Medical School, Boston, MA, USA]
 
* ENA, European Nucleotide Archive:<br />[http://www.ebi.ac.uk/embl/ ENA, European Nucleotide Archive, EMBL-EBI, Cambridge, UK]
 
* ENA, European Nucleotide Archive:<br />[http://www.ebi.ac.uk/embl/ ENA, European Nucleotide Archive, EMBL-EBI, Cambridge, UK]
 +
* EPD, the Eukaryotic Promoter Database:<br />[http://www.epd.isb-sib.ch/ EPD, Epalinges s/Lausanne, Switzerland]
 
* euGenes, Genomic Information for Eukaryotic Organisms, including Drosophila:<br />[http://iubio.bio.indiana.edu/eugenes/  euGenes, Indiana University, USA]
 
* euGenes, Genomic Information for Eukaryotic Organisms, including Drosophila:<br />[http://iubio.bio.indiana.edu/eugenes/  euGenes, Indiana University, USA]
 
* EvoPrinter, Identification of Evolutionarily Resilient DNA Sequences<br />[http://evoprinter.ninds.nih.gov/ NINDS, NIH, Bethesda MD, USA]
 
* EvoPrinter, Identification of Evolutionarily Resilient DNA Sequences<br />[http://evoprinter.ninds.nih.gov/ NINDS, NIH, Bethesda MD, USA]
 +
* FlyAtlas, the Drosophila adult gene expression atlas:<br />[http://www.flyatlas.org/ FlyAtlas, University of Glasgow, UK]
 
* FlyMine, an integrated database for Drosophila &amp; Anopheles genomics:<br />[http://www.flymine.org/ University of Cambridge, United Kingdom]
 
* FlyMine, an integrated database for Drosophila &amp; Anopheles genomics:<br />[http://www.flymine.org/ University of Cambridge, United Kingdom]
 
* FlyPhenomics, phenotypic differences between species of the ''D. melanogaster'' subgroup:<br />[http://www.normalesup.org/~vorgogoz/FlyPhenomics/ FlyPhenomics, Paris, France]
 
* FlyPhenomics, phenotypic differences between species of the ''D. melanogaster'' subgroup:<br />[http://www.normalesup.org/~vorgogoz/FlyPhenomics/ FlyPhenomics, Paris, France]
 
* FlySNP Project:<br />[http://flysnp.imp.univie.ac.at/ FlySNP, Austrian Academy of Sciences, Austria]
 
* FlySNP Project:<br />[http://flysnp.imp.univie.ac.at/ FlySNP, Austrian Academy of Sciences, Austria]
* Galaxy:<br />[https://usegalaxy.org/ Galaxy, Penn State, PA USA and Emory University, GA USA]
+
* Galaxy: Open Source Bioinformatics Tools<br />[https://usegalaxy.org/ Galaxy, Penn State, PA USA and Emory University, GA USA]
 
* GenBank,the NIH genetic sequence database:<br />[http://www.ncbi.nlm.nih.gov/Genbank/ GenBank, NCBI, Bethesda, MD USA]
 
* GenBank,the NIH genetic sequence database:<br />[http://www.ncbi.nlm.nih.gov/Genbank/ GenBank, NCBI, Bethesda, MD USA]
 
* GenomeRNAi, Heidelberg, a database of RNA interference (RNAi) screens in cultured Drosophila cells:<br />[http://www.dkfz.de/signaling2/rnai/index.php GenomeRNAi, DKFZ, Heidelberg, Germany]
 
* GenomeRNAi, Heidelberg, a database of RNA interference (RNAi) screens in cultured Drosophila cells:<br />[http://www.dkfz.de/signaling2/rnai/index.php GenomeRNAi, DKFZ, Heidelberg, Germany]
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* Mitotic Spindle Assembly Database:<br />[http://rnai.ucsf.edu/mitospindlescreen/index.html Genes Required for Mitotic Spindle Assembly in S2 cells, University of California, San Francisco, USA]
 
* Mitotic Spindle Assembly Database:<br />[http://rnai.ucsf.edu/mitospindlescreen/index.html Genes Required for Mitotic Spindle Assembly in S2 cells, University of California, San Francisco, USA]
 
* NHGRI Drosophila Genome Sequencing Proposals, Status of Sequencing:<br />[http://www.genome.gov/ National Human Genome Research Institute, Bethesda, MD, USA]
 
* NHGRI Drosophila Genome Sequencing Proposals, Status of Sequencing:<br />[http://www.genome.gov/ National Human Genome Research Institute, Bethesda, MD, USA]
 +
* OnTheFly, Database of Drosophila Transcription Factors and Transcription Factor Binding Sites <br />[https://bhapp.c2b2.columbia.edu/OnTheFly/index.php Columbia University, USA]
 
* Panther protein classification system:<br />[http://panther.appliedbiosystems.com/about.jsp Panther Protein Classification System, Applied Biosystems &amp; Celera, USA]
 
* Panther protein classification system:<br />[http://panther.appliedbiosystems.com/about.jsp Panther Protein Classification System, Applied Biosystems &amp; Celera, USA]
 
* PDB, Protein Data Bank:<br />[http://www.rcsb.org/pdb/home/home.do PDB, The Research Collaboratory for Structural Bioinformatics (RCSB) consortium]
 
* PDB, Protein Data Bank:<br />[http://www.rcsb.org/pdb/home/home.do PDB, The Research Collaboratory for Structural Bioinformatics (RCSB) consortium]
 
* PhospoPep - phosphorylation site data from ''D. melanogaster'' cell lines:<br />[http://www.phosphopep.org/ The Aebersold group at the ETH in collaboration with the FGCZ in Switzerland, and the ISB, USA.]
 
* PhospoPep - phosphorylation site data from ''D. melanogaster'' cell lines:<br />[http://www.phosphopep.org/ The Aebersold group at the ETH in collaboration with the FGCZ in Switzerland, and the ISB, USA.]
 
* PubMed, Biomedical literature citations and abstracts:<br />[http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed PubMed, NCBI, Bethesda, MD USA]
 
* PubMed, Biomedical literature citations and abstracts:<br />[http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed PubMed, NCBI, Bethesda, MD USA]
 +
* REDfly, Regulatory Element Database for Drosophila:<br />[http://redfly.ccr.buffalo.edu/ REDfly, University at Buffalo, New York, USA]
 
* Rfam, RNA families database of alignments and CMs:<br />[http://www.webcitation.org/getfile?fileid=db1c351a4c279e9cf9697bd2d1962097900701fb Rfam, the Sanger Institute, Cambridge, UK and Janelia Farm, Ashburn, VA, USA]
 
* Rfam, RNA families database of alignments and CMs:<br />[http://www.webcitation.org/getfile?fileid=db1c351a4c279e9cf9697bd2d1962097900701fb Rfam, the Sanger Institute, Cambridge, UK and Janelia Farm, Ashburn, VA, USA]
 
* SMART, Simple Modular Architecture Research Tool:<br />[http://smart.embl-heidelberg.de/ SMART, EMBL, Heidleberg]
 
* SMART, Simple Modular Architecture Research Tool:<br />[http://smart.embl-heidelberg.de/ SMART, EMBL, Heidleberg]
 
* TaxoDros, the database on Taxonomy of Drosophilidae:<br />[http://www.taxodros.uzh.ch/ TaxoDros, University of Zurich, Switzerland]
 
* TaxoDros, the database on Taxonomy of Drosophilidae:<br />[http://www.taxodros.uzh.ch/ TaxoDros, University of Zurich, Switzerland]
 +
* The Drosophila Transcription Factor Database:<br />[http://www.flytf.org/ FlyTF.org, MRC Cambridge, UK]
 +
* TRANSFAC, A database of transcription factors and their binding sites:<br />[http://www.gene-regulation.com/pub/databases.html#transfac TRANSFAC, Braunschweig, Germany]
 
* UniProtKB, a comprehensive catalog of information on proteins:<br />[http://www.pir.uniprot.org/ UniProtKB, The UniProt Consortium]
 
* UniProtKB, a comprehensive catalog of information on proteins:<br />[http://www.pir.uniprot.org/ UniProtKB, The UniProt Consortium]
 
* Whole Genome Comparative Analysis of the D. melanogaster (CAF1) Genome''<nowiki>:</nowiki><br />[http://pipeline.lbl.gov/cgi-bin/gateway2?bg=droMel_caf1&selector=vistapoint Vista Tools for Comparative Genomics, LBNL, USA]
 
* Whole Genome Comparative Analysis of the D. melanogaster (CAF1) Genome''<nowiki>:</nowiki><br />[http://pipeline.lbl.gov/cgi-bin/gateway2?bg=droMel_caf1&selector=vistapoint Vista Tools for Comparative Genomics, LBNL, USA]
 
=Transcription Regulation Databases=
 
* BDTNP, ChIP/chip in vivo DNA binding data:<br />[http://bdtnp.lbl.gov/Fly-Net/chipchip.jsp?w=summary Berkeley Drosophila Transcription Network Project, University of California, Berkeley, USA]
 
* DNase I Footprint Database<nowiki>: </nowiki><br />[http://www.flyreg.org/ University of Manchester Bioinformatics Resources, University of Manchester, UK]
 
* EPD, the Eukaryotic Promoter Database:<br />[http://www.epd.isb-sib.ch/ EPD, Epalinges s/Lausanne, Switzerland]
 
* OnTheFly, Database of Drosophila Transcription Factors and Transcription Factor Binding Sites <br />[https://bhapp.c2b2.columbia.edu/OnTheFly/index.php Columbia University, USA]
 
* REDfly, Regulatory Element Database for Drosophila:<br />[http://redfly.ccr.buffalo.edu/ REDfly, University at Buffalo, New York, USA]
 
* The Drosophila Transcription Factor Database:<br />[http://www.flytf.org/ FlyTF.org, MRC Cambridge, UK]
 
* TRANSFAC, A database of transcription factors and their binding sites:<br />[http://www.gene-regulation.com/pub/databases.html#transfac TRANSFAC, Braunschweig, Germany]
 
 
=Genetic and Protein Interaction Databases=
 
* BioGRID, The General Repository for Interaction Datasets<br />[http://www.thebiogrid.org/index.php BioGRID, Mount Sinai Hospital, Toronto, Canada]
 
* DPiM, Drosophila Protein interaction Map<br />[https://interfly.med.harvard.edu/ DPiM, Harvard University Medical School, Boston, MA, USA]
 
* DroID, Drosophila Interactions Database<br />[http://www.droidb.org/ Drosophila Interaction Database, Detroit, USA]
 
* Drosophila PIMRider, Drosophila Protein Interaction Map<br />[https://pimr.hybrigenics.com/htmlFiles/interactionData/drosophila.html Drosophila PIMRider, Hybrigenics, Paris, France]
 
* IM Browser, Drosophila Interactions Database<br />[http://proteome.wayne.edu/PIMdb.html IM Browser, Wayne State University, Detroit, MI, USA]
 
* STRING, Known and Predicted Protein-Protein Interactions<br />[http://string-db.org/ STRING]
 
  
 
=Data and Metadata for Drosophila Genomes=
 
=Data and Metadata for Drosophila Genomes=
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* ''D. willistoni'' Genome:<br />[http://www.ncbi.nlm.nih.gov/genome/251' D. willistoni Organism Overview, NCBI, USA]<br />[http://www.ebi.ac.uk/ena/data/view/GCA_000005925 D. willistoni Genome Assembly Report, ENA, UK]
 
* ''D. willistoni'' Genome:<br />[http://www.ncbi.nlm.nih.gov/genome/251' D. willistoni Organism Overview, NCBI, USA]<br />[http://www.ebi.ac.uk/ena/data/view/GCA_000005925 D. willistoni Genome Assembly Report, ENA, UK]
 
* ''D. yakuba'' Genome:<br />[http://www.ncbi.nlm.nih.gov/genome/148' D. yakuba Organism Overview, NCBI, USA]<br />[http://www.ebi.ac.uk/ena/data/view/GCA_000005975 D. yakuba Genome Assembly Report, ENA, UK]
 
* ''D. yakuba'' Genome:<br />[http://www.ncbi.nlm.nih.gov/genome/148' D. yakuba Organism Overview, NCBI, USA]<br />[http://www.ebi.ac.uk/ena/data/view/GCA_000005975 D. yakuba Genome Assembly Report, ENA, UK]
 +
 +
=Genetic and Protein Interaction Databases=
 +
* BioGRID, The General Repository for Interaction Datasets<br />[http://www.thebiogrid.org/index.php BioGRID, Mount Sinai Hospital, Toronto, Canada]
 +
* DPiM, Drosophila Protein interaction Map<br />[https://interfly.med.harvard.edu/ DPiM, Harvard University Medical School, Boston, MA, USA]
 +
* DroID, Drosophila Interactions Database<br />[http://www.droidb.org/ Drosophila Interaction Database, Detroit, USA]
 +
* Drosophila PIMRider, Drosophila Protein Interaction Map<br />[https://pimr.hybrigenics.com/htmlFiles/interactionData/drosophila.html Drosophila PIMRider, Hybrigenics, Paris, France]
 +
* IM Browser, Drosophila Interactions Database<br />[http://proteome.wayne.edu/PIMdb.html IM Browser, Wayne State University, Detroit, MI, USA]
 +
* STRING, Known and Predicted Protein-Protein Interactions<br />[http://string-db.org/ STRING]
 +
  
 
=Sequence Analysis=
 
=Sequence Analysis=

Revision as of 15:01, 16 October 2014

Comparative Analyses and Genome Databases

Data and Metadata for Drosophila Genomes

Genetic and Protein Interaction Databases


Sequence Analysis

Atlases, Images, and Videos

Other