Difference between revisions of "FlyBase:Drosophila Online Resources"
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* GEO, NCBI's Gene Expression Omnibus:<br />[http://www.ncbi.nlm.nih.gov/geo/ GEO, NCBI, Bethesda, MD USA] | * 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] | * 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] | ||
| + | * Homophila, Human Disease to Drosophila Gene Database:<br />[http://superfly.ucsd.edu/homophila/ Homophila, San Diego, USA] | ||
| + | * InParanoid, Eukaryotic Ortholog Groups:<br />[http://inparanoid.sbc.su.se/cgi-bin/index.cgi InParanoid, Karolinska Institute, Sweden] | ||
| + | * InterPro protein domain analysis of Drosophila:<br />[http://www.ebi.ac.uk/integr8/InterproAnalysisPage.do?orgProteomeID=17 InterPro proteome analysis, EBI, UK] | ||
| + | * MANTiS a phylogenetic framework for multi-species genome comparisons:<br />[http://www.mantisdb.org/MANTiS/Welcome.html MANTiS, Université Libre de Bruxelles, Belgium] | ||
| + | * MEROPS, an information resource for peptidases:<br />[http://merops.sanger.ac.uk/ MEROPS, The Sanger Institute, Cambridge, UK] | ||
| + | * miRBase, microRNA data:<br />[http://microrna.sanger.ac.uk/sequences/index.shtml miRBase, The Sanger Institute, Cambridge, UK] | ||
| + | * MitoDrome, ''Drosophila melanogaster'' nuclear genes encoding for mitochondrial proteins:<br />[http://www2.ba.itb.cnr.it/MitoDrome/ MitoDrome, Bari, Italy] | ||
| + | * 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://genome.gov/page.cfm?pageID=10002154 National Human Genome Research Institute, Bethesda, MD, USA] | ||
| + | * Panther protein classification system:<br />[http://panther.appliedbiosystems.com/about.jsp Panther Protein Classification System, Applied Biosystems & Celera, USA] | ||
| + | * 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.] | ||
| + | * Proteome analysis of Drosophila:<br />[http://www.ebi.ac.uk/integr8/ProteomeAnalysisAction.do?orgProteomeID=17 Proteome analysis, EBI, UK] | ||
| + | * 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.sanger.ac.uk/Software/Rfam/ Rfam, the Sanger Institute, Cambridge, UK and Janelia Farm, Ashburn, VA, USA] | ||
| + | * Sebida, Sex Bias Database:<br />[http://141.61.102.16:8080/sebida/index.php Sebida, MPI Martinsried, Germany] | ||
| + | * TaxoDros, the database on Taxonomy of Drosophilidae:<br />[http://taxodros.unizh.ch/ TaxoDros, University of Zurich, Switzerland] | ||
| + | * The Drosophila Transcription Factor Database:<br />[http://www.flytf.org/ FlyTF.org, MRC Cambridge, UK] | ||
| + | * The McGill ''Drosophila melanogaster'' Genome Project:<br />[http://www.mcgill.ca/Biology/labs/MDGP/home.html McGill Drosophila Genome Project, Canada] | ||
| + | * TRANSFAC, A database of transcription factors and their binding sites:<br />[http://www.gene-regulation.com/pub/databases.html#transfac TRANSFAC, Braunschweig, Germany] | ||
| + | * TransTerm, a Translational Signal Database:<br />[http://uther.otago.ac.nz/Transterm.html TransTerm, Dunedin, New Zealand] | ||
| + | * UniProtKB, a comprehensive catalog of information on proteins:<br />[http://www.pir.uniprot.org/ UniProtKB, The UniProt Consortium] | ||
| + | * Whole genome comparative analysis of ''D. melanogaster'' and ''D. pseudoobscura''<nowiki>:</nowiki><br />[http://pipeline.lbl.gov/pseudo/ Whole genome analysis, LBNL, USA] | ||
=Sequence Traces of Drosophila Genomes= | =Sequence Traces of Drosophila Genomes= | ||
Revision as of 14:55, 17 April 2014
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:
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 - 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 - 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
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