Difference between revisions of "FlyBase:Drosophila Online Resources"
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| − | + | * Assembly/Alignment/Annotation of 12 related Drosophila species:<br />[http://rana.lbl.gov/drosophila/ Assembly/Alignment/Annotation, LBNL, 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] |
| − | * | + | * 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] |
| − | * | + | * 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 />[http://www.hgsc.bcm.tmc.edu/projects/drosophila/ Human Genome Sequencing Center, Baylor College of Medicine, USA] |
| − | * | + | * ''D. simulans'' genome project:<br />[http://genome.wustl.edu/genome.cgi?GENOME=Drosophila simulans White 501 Genome Sequencing Center, Washington University, USA] |
| − | * | + | * ''D. yakuba'' genome project:<br />[http://genome.wustl.edu/genome.cgi?GENOME=Drosophila yakuba Genome Sequencing Center, Washington University, USA] |
| − | * | + | * ''D. melanogaster'' UCSC Genome Browser Gateway:<br />[http://genome.ucsc.edu/cgi-bin/hgGateway?org=D. melanogaster&db=0 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] |
| − | * | + | * DNase I Footprint Database<nowiki>: </nowiki><br />[http://www.flyreg.org/ University of Manchester Bioinformatics Resources, University of Manchester, UK] |
| − | * | + | * Drosophila Heterochromatin Genome Project (DHGP):<br />[http://dhgp.org/ DHGP, Lawrence Berkeley National Laboratory, USA] |
| − | * | + | * ''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 Population Genomic Project (DPGP):<br />[http://www.dpgp.org/ DPGP, University of California, Davis, USA] |
| − | * | + | * Drosophila simulans and yakuba sequencing projects:<br />[http://www.dpgp.org/sim_yak/index.html DPGP, University of California, Davis, USA] |
| − | * | + | * Drosophilidae Taxonomic Database:<br />[http://bioinfo.lowtem.hokudai.ac.jp/db/modules/stdb/ Drosophilidae Taxonomic Database, Japan] |
| − | * | + | * Drosophilidae Taxonomy - Collection of Papers:<br />[http://www.dgrc.kit.ac.jp/~jdd/class/index.html Japan Drosophila Database (JDD) on Taxonomy, Japan] |
| − | * | + | * DRSC, Drosophila RNAi Screening Center:<br />[http://www.flyrnai.org/index.html DRSC, Harvard Medical School, Boston, MA, USA] |
| − | * | + | * EMBL Nucleotide Sequence Database:<br />[http://www.ebi.ac.uk/embl/ EMBL Nucleotide Sequence Database, 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] |
| − | * | + | * EvoPrinter, Identification of Evolutionarily Resilient DNA Sequences<br />[http://evoprinter.ninds.nih.gov/ NINDS, NIH, Bethesda MD, USA] |
| − | * | + | * FLIGHT, Fly database for the Integration of Genomic and High-Throughput data:<br />[http://flight.licr.org/ FLIGHT Database, Ludwig Institute for Cancer Research, London, UK] |
| − | * | + | * FlyAtlas, the Drosophila adult gene expression atlas:<br />[http://www.flyatlas.org/ FlyAtlas, University of Glasgow, UK] |
| − | * | + | * FlyMine, an integrated database for Drosophila & 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] |
| − | * | + | * FlySNP Project:<br />[http://flysnp.imp.univie.ac.at/ FlySNP, Austrian Academy of Sciences, Austria] |
| − | * | + | * 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] |
| − | * | + | * GEO, NCBI's Gene Expression Omnibus:<br />[http://www.ncbi.nlm.nih.gov/geo/ GEO, NCBI, Bethesda, MD USA] |
| − | * | + | * GPCRDB, information system for G protein-coupled receptors (GPCRs):<br />[http://www.gpcr.org/7tm/ GPCRDB, The GPCRDB (G Protein-Coupled Receptor Data Base) partnership] |
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=Sequence Traces of Drosophila Genomes= | =Sequence Traces of Drosophila Genomes= | ||
Revision as of 14:48, 17 April 2014
- 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:
simulans White 501 Genome Sequencing Center, Washington University, USA - D. yakuba genome project:
yakuba Genome Sequencing Center, Washington University, USA - D. melanogaster UCSC Genome Browser Gateway:
melanogaster&db=0 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
Sequence Traces of Drosophila Genomes
- D. ananassae genomic sequence trace archives:
ANANASSAE' NCBI Trace Archives, USA
Ensembl FTP Trace Repository, EBI, UK - D. erecta genomic sequence trace archives:
ERECTA' NCBI Trace Archives, USA
Ensembl FTP Trace Repository, EBI, UK - D. grimshawi genomic sequence trace archives:
GRIMSHAWI' NCBI Trace Archives, USA
Ensembl FTP Trace Repository, EBI, UK - D. melanogaster genomic sequence trace archives:
MELANOGASTER' NCBI Trace Archives, USA
Ensembl FTP Trace Repository, EBI, UK - D. mojavensis genomic sequence trace archives:
MOJAVENSIS' NCBI Trace Archives, USA
Ensembl FTP Trace Repository, EBI, UK - D. persimilis genomic sequence trace archives:
PERSIMILIS' NCBI Trace Archives, USA
Ensembl FTP Trace Repository, EBI, UK - D. pseudoobscura genomic sequence trace archives:
PSEUDOOBSCURA' NCBI Trace Archives, USA
Ensembl FTP Trace Repository, EBI, UK - D. sechellia genomic sequence trace archives:
SECHELLIA' NCBI Trace Archives, USA
Ensembl FTP Trace Repository, EBI, UK - D. simulans genomic sequence trace archives:
SIMULANS' NCBI Trace Archives, USA
Ensembl FTP Trace Repository, EBI, UK - D. virilis genomic sequence trace archives:
VIRILIS' NCBI Trace Archives, USA
Ensembl FTP Trace Repository, EBI, UK - D. willistoni genomic sequence trace archives:
WILLISTONI' NCBI Trace Archives, USA
Ensembl FTP Trace Repository, EBI, UK - D. yakuba genomic sequence trace archives:
YAKUBA' NCBI Trace Archives, USA
Ensembl FTP Trace Repository, EBI, UK
Genetic and Protein Interaction Databases
- BioGRID, The General Repository for Interaction Datasets
BioGRID, Mount Sinai Hospital, Toronto, Canada - 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 - IM Browser, Drosophila Interactions Database
IM Browser, Wayne State University, Detroit, MI, USA
Sequence Analysis
- Apollo, a genome annotation viewer and editor:
Apollo - cis-analyst, to search the Drosophila genome for clusters of binding sites:
cis-analyst, USA - FlyPrimerBank, a comprehensive qPCR primer database for Drosophila:
FlyPrimerBank, USA - Gene-Finder for Drosophila:
Gene Finding, FGENESH, SoftBerry - GenePalette, a tool for genome sequence visualization and navigation:
GenePalette, University of California, San Diego, USA - Genie Gene finder for Drosophila:
Genie, USA - miRNA, Target Gene Prediction:
miRNA - Target Prediction, EMBL, Heidelberg, Germany - miRNA_Targets:
miRNA targets on full length mRNAs, Deakin University, Victoria, Australia - Neural Network Promoter Prediction for Drosophila:
Neural Network Promoter Prediction, USA - PREdictor, to identify Polycomb/Trithorax response elements:
PREdictor, Bielefeld University, Germany - Splice Site Prediction for Drosophila:
Splice Site Prediction, USA - Stubb site, to find clusters of cis-regulatory binding sites:
Stubb web site, Rockefeller University, New York, USA - Target Explorer, to identify clusters of transcription factor binding sites:
Target Explorer, Columbia University, New York, USA - UP-TORR Fly, a tool for identifying updated targets of RNAi reagents:
Updated Targets of RNAi Reagents, USA
Atlases, Images, and Videos
- BDTNP, A cellular resolution 3D gene expression and morphology Atlas of the blastoderm.
BDTNP, University of California, Berkeley, USA - CSIRO Entomology Anatomical Atlas of Flies:
CSIRO Entomology, Australia - Electron micrograph maps of Drosophila melanogaster polytene chromosomes:
Sorsa Maps, Helsinki, Finland - Fly Motor Axon Page:
home page.html Motor Axon, California Institute of Technology, USA - 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 - FlyEx, a Database of Segmentation Gene Expression in Drosophila:
FlyEx, St. Petersburg State Polytechnical University, Russia
FlyEx, Stony Brook University, USA - FlyExpress, an Expression Pattern Search Engine:
FlyExpress, Arizona State University, USA - FlyLight, Expression Patterns of GAL4 Driver Lines:
HHMI, Janelia Farms Research Campus - FlyMove, an Image, Movie and Interactive Shockwave Resource:
FlyMove, Muenster, Germany - FlyTrap, a GFP Protein Trap Database:
FlyTrap, Yale University, USA - flytrap, a database of P{GAL4} enhancer traps and their expression in brains:
flytrap, University of Edinburgh, UK - FlyView, a Drosophila Image Database:
FlyView, Muenster, Germany - GETDB, a Gal4 enhancer trap database:
GETDB, National Institute of Basic Biology, Okazaki, Japan - Jove, videos of experimental techniques:
Jove, Journal of Visualized Experiments, USA - Patterns of gene expression in Drosophila embryogenesis:
Gene expression database, BDGP, 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:
Edinburgh & Cambridge, UK