Difference between revisions of "FlyBase:Drosophila Online Resources"
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=Sequence Analysis= | =Sequence Analysis= | ||
| + | * <span class="bold">Apollo</span>, a genome annotation viewer and editor: <br />[http://apollo.berkeleybop.org/current/index.html Apollo] | ||
| + | * <span class="bold">cis-analyst</span>, to search the Drosophila genome for clusters of binding sites: <br />[http://rana.lbl.gov/cis-analyst/ cis-analyst, USA] | ||
| + | * <span class="bold">FlyPrimerBank</span>, a comprehensive qPCR primer database for Drosophila: <br />[http://www.flyrnai.org/FlyPrimerBank FlyPrimerBank, USA] | ||
| + | * <span class="bold">Gene-Finder for Drosophila:</span><br />[http://www.softberry.com/berry.phtml?topic=gfind&prg=FGENESH Gene Finding, FGENESH, SoftBerry] | ||
| + | * <span class="bold">GenePalette</span>, a tool for genome sequence visualization and navigation: <br />[http://www.genepalette.org/ GenePalette, University of California, San Diego, USA] | ||
| + | * <span class="bold">Genie Gene finder for Drosophila:</span><br />[http://www.fruitfly.org/seq_tools/genie.html Genie, USA] | ||
| + | * <span class="bold">miRNA, Target Gene Prediction:</span><br />[http://www.mirna.embl.de/ miRNA - Target Prediction, EMBL, Heidelberg, Germany] | ||
| + | * <span class="bold">miRNA_Targets:</span><br />[http://mamsap.it.deakin.edu.au/~amitkuma/mirna_targetsnew/index.html miRNA targets on full length mRNAs, Deakin University, Victoria, Australia] | ||
| + | * <span class="bold">Neural Network Promoter Prediction for Drosophila:</span><br />[http://www.fruitfly.org/seq_tools/promoter.html Neural Network Promoter Prediction, USA] | ||
| + | * <span class="bold">PREdictor</span>, to identify Polycomb/Trithorax response elements: <br />[http://bibiserv.techfak.uni-bielefeld.de/predictor/ PREdictor, Bielefeld University, Germany] | ||
| + | * <span class="bold">Splice Site Prediction for Drosophila:</span><br />[http://www.fruitfly.org/seq_tools/splice.html Splice Site Prediction, USA] | ||
| + | * <span class="bold">Stubb site</span>, to find clusters of cis-regulatory binding sites: <br />[http://stubb.rockefeller.edu/ Stubb web site, Rockefeller University, New York, USA] | ||
| + | * <span class="bold">Target Explorer</span>, to identify clusters of transcription factor binding sites: <br />[http://trantor.bioc.columbia.edu/Target_Explorer/ Target Explorer, Columbia University, New York, USA] | ||
| + | * <span class="bold">UP-TORR Fly</span>, a tool for identifying updated targets of RNAi reagents: <br />[http://www.flyrnai.org/up-torr/ Updated Targets of RNAi Reagents, USA] | ||
| + | |||
=Atlases, Images, and Videos= | =Atlases, Images, and Videos= | ||
=Other= | =Other= | ||
Revision as of 14:45, 17 April 2014
Comparative Analysises 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