Difference between revisions of "FlyBase:Drosophila Online Resources"
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* FGENESH, Annotation of animal genomes-genes, promoters, functional motifs, protein sub-cellular localization.:<br />[http://www.softberry.com/berry.phtml?topic=case_study_animal&no_menu=on Annotation of genomes, Softberry, USA] | * FGENESH, Annotation of animal genomes-genes, promoters, functional motifs, protein sub-cellular localization.:<br />[http://www.softberry.com/berry.phtml?topic=case_study_animal&no_menu=on Annotation of genomes, Softberry, USA] | ||
* GenePalette, a tool for genome sequence visualization and navigation: <br />[http://www.genepalette.org/ GenePalette, University of California, San Diego, USA] | * GenePalette, a tool for genome sequence visualization and navigation: <br />[http://www.genepalette.org/ GenePalette, University of California, San Diego, USA] | ||
| − | * Genie Gene finder for Drosophila:<br />[http://www.fruitfly.org/seq_tools/genie.html Genie, USA] | + | * Genie Gene finder for Drosophila:<br />[http://www.fruitfly.org/seq_tools/genie.html Genie, Berkeley Drosophila Genome Project, University of California, Berkeley, USA] |
* miRNA, Target Gene Prediction:<br />[http://www.mirna.embl.de/ miRNA - Target Prediction, EMBL, Heidelberg, Germany] | * miRNA, Target Gene Prediction:<br />[http://www.mirna.embl.de/ miRNA - Target Prediction, EMBL, Heidelberg, Germany] | ||
* miRNA_Targets:<br />[http://mamsap.it.deakin.edu.au/~amitkuma/mirna_targetsnew/index.html miRNA targets on full length mRNAs, Deakin University, Victoria, Australia] | * miRNA_Targets:<br />[http://mamsap.it.deakin.edu.au/~amitkuma/mirna_targetsnew/index.html miRNA targets on full length mRNAs, Deakin University, Victoria, Australia] | ||
| − | * Neural Network Promoter Prediction for Drosophila:<br />[http://www.fruitfly.org/seq_tools/promoter.html Neural Network Promoter Prediction, USA] | + | * Neural Network Promoter Prediction for Drosophila:<br />[http://www.fruitfly.org/seq_tools/promoter.html Neural Network Promoter Prediction, Berkeley Drosophila Genome Project, University of California, Berkeley, USA] |
* PREdictor, to identify Polycomb/Trithorax response elements: <br />[http://bibiserv.techfak.uni-bielefeld.de/predictor/ PREdictor, Bielefeld University, Germany] | * PREdictor, to identify Polycomb/Trithorax response elements: <br />[http://bibiserv.techfak.uni-bielefeld.de/predictor/ PREdictor, Bielefeld University, Germany] | ||
| − | * Splice Site Prediction for Drosophila:<br />[http://www.fruitfly.org/seq_tools/splice.html Splice Site Prediction, USA] | + | * Splice Site Prediction for Drosophila:<br />[http://www.fruitfly.org/seq_tools/splice.html Splice Site Prediction, Berkeley Drosophila Genome Project, University of California, Berkeley, USA] |
* Stubb site, to find clusters of cis-regulatory binding sites: <br />[http://stubb.rockefeller.edu/ Stubb web site, Rockefeller University, New York, USA] | * Stubb site, to find clusters of cis-regulatory binding sites: <br />[http://stubb.rockefeller.edu/ Stubb web site, Rockefeller University, New York, USA] | ||
* Target Explorer, to identify clusters of transcription factor binding sites: <br />[http://trantor.bioc.columbia.edu/Target_Explorer/ Target Explorer, Columbia University, New York, USA] | * Target Explorer, to identify clusters of transcription factor binding sites: <br />[http://trantor.bioc.columbia.edu/Target_Explorer/ Target Explorer, Columbia University, New York, USA] | ||
Revision as of 21:14, 14 October 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:
pseudoobscura 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, UCSC Genome Browser, 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 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 - ENA, European Nucleotide Archive:
ENA, European Nucleotide Archive, EMBL-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 - 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: protein sequence analysis & classification, 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. - 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 - TaxoDros, the database on Taxonomy of Drosophilidae:
TaxoDros, University of Zurich, Switzerland - The Drosophila Transcription Factor Database:
FlyTF.org, MRC Cambridge, UK - TRANSFAC, A database of transcription factors and their binding sites:
TRANSFAC, Braunschweig, Germany - UniProtKB, a comprehensive catalog of information on proteins:
UniProtKB, The UniProt Consortium - Whole Genome Comparative Analysis of the D. melanogaster (CAF1) Genome:
Vista Tools for Comparative Genomics, 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
- cis-analyst, to search the Drosophila genome for clusters of binding sites:
cis-analyst, USA - FlyPrimerBank, a comprehensive qPCR primer database for Drosophila:
FlyPrimerBank, DRSC, Harvard Medical School, Boston, MA, USA - FGENESH, Annotation of animal genomes-genes, promoters, functional motifs, protein sub-cellular localization.:
Annotation of genomes, Softberry, USA - GenePalette, a tool for genome sequence visualization and navigation:
GenePalette, University of California, San Diego, USA - Genie Gene finder for Drosophila:
Genie, Berkeley Drosophila Genome Project, University of California, Berkeley, 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, Berkeley Drosophila Genome Project, University of California, Berkeley, USA - PREdictor, to identify Polycomb/Trithorax response elements:
PREdictor, Bielefeld University, Germany - Splice Site Prediction for Drosophila:
Splice Site Prediction, Berkeley Drosophila Genome Project, University of California, Berkeley, 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 - Web Apollo, a collaborative genomic annotation editor:
Web Apollo
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
Other
- Drosophila Information Service:
DIS, Norman, Oklahoma, USA - FlyNome, a database of Drosophila nomenclature:
FlyNome, USA - FlyPNS, embryonic and larval peripheral nervous system:
FlyPNS, USA - FlyTree, the Drosophila Researcher Genealogy has been incorporated into the Academic Tree Project:
FlyTree, USA - Interactive Fly, A cyberspace guide to Drosophila development and metazoan evolution
Interactive Fly, Bethesda, MD, USA - Jfly , a data depository for the fly and other insects, with an emphasis for the Japanese-speaking fly community:
Jfly, University of Tokyo, Japan - The WWW Virtual Library--Drosophila:
Drosophila Virtual Library - Tracheal Database, information on tracheal development in Drosophila:
Tracheal Database, Switzerland