Difference between revisions of "FlyBase:Drosophila Online Resources"
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* 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] | * 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] | ||
* Web Apollo, a collaborative genomic annotation editor: <br />[http://apollo.berkeleybop.org/ Web Apollo, LBL, Berkeley, USA] | * Web Apollo, a collaborative genomic annotation editor: <br />[http://apollo.berkeleybop.org/ Web Apollo, LBL, Berkeley, USA] | ||
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=Taxonomy= | =Taxonomy= | ||
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* 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] | * 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] | ||
* cis-analyst, to search the Drosophila genome for clusters of binding sites: <br />[http://rana.lbl.gov/cis-analyst/ cis-analyst, USA] | * cis-analyst, to search the Drosophila genome for clusters of binding sites: <br />[http://rana.lbl.gov/cis-analyst/ cis-analyst, USA] | ||
| − | * DNase I Footprint Database<nowiki>: </nowiki><br />[http://www.flyreg.org/ University of Manchester Bioinformatics Resources, University of Manchester, UK] | + | * DBD: Transcription factor prediction database: <br />[http://www.transcriptionfactor.org/index.cgi?Home DBD] |
| + | * 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] | * EPD, the Eukaryotic Promoter Database:<br />[http://www.epd.isb-sib.ch/ EPD, Epalinges s/Lausanne, Switzerland] | ||
| + | * Fly Factor Survey - Database of Drosophila TF DNA-binding Specificitiies: <br />[http://pgfe.umassmed.edu/ffs/ FLy Factor Survey, UMass Medical School, Worcester, MA, USA] | ||
* OnTheFly, Database of Drosophila Transcription Factors and Transcription Factor Binding Sites <br />[https://bhapp.c2b2.columbia.edu/OnTheFly/index.php Columbia University, USA] | * OnTheFly, Database of Drosophila Transcription Factors and Transcription Factor Binding Sites <br />[https://bhapp.c2b2.columbia.edu/OnTheFly/index.php Columbia University, 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] | * 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] | ||
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* The Drosophila Transcription Factor Database:<br />[http://www.flytf.org/ FlyTF.org, MRC Cambridge, UK] | * 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] | * TRANSFAC, A database of transcription factors and their binding sites:<br />[http://www.gene-regulation.com/pub/databases.html#transfac TRANSFAC, Braunschweig, Germany] | ||
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[[Category:DONE]] | [[Category:DONE]] | ||
Revision as of 17:58, 6 November 2014
Atlases, Images and Videos
- BDTNP, A cellular resolution 3D gene expression and morphology Atlas of the blastoderm.
Berkeley Drosophila Transcription Network Project, University of California, Berkeley, USA - CSIRO Anatomical Atlas of Flies:
CSIRO Entomology, Australia - Electron micrograph maps of Drosophila melanogaster polytene chromosomes:
Sorsa Maps, Helsinki, Finland - 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 - FlyMove, an Image, Movie and Interactive Shockwave Resource:
FlyMove, Muenster, Germany - FlyPNS, D. melanogaster embryonic and larval peripheral nervous system:
FlyPNS, UMPC, Paris, France and Columbia University, NY, USA - 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 - 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:
Virtual Fly Brain, Edinburgh and Cambridge, UK
Data Repositories
- Array Express - Functional Genomics Data:
EMBL-EBI, Cambridge, UK - Berkeley Drosophila Genome Project (BDGP):
BDGP, University of California, Berkeley, USA - DDBJ, the DNA Data Bank of Japan:
DDBJ, National Institute of Genetics, Mishima, Japan - EMBL-EBI, The European Bioinformatics Institute:
EMBL-EBI,Hinxton, UK - ENA, European Nucleotide Archive:
ENA, European Nucleotide Archive, EMBL-EBI, Cambridge, UK - Ensembl Genome Browser:
EMBL-EBI, Hinxton, UK - GenBank,the NIH genetic sequence database:
GenBank, NCBI, Bethesda, MD USA - GEO Datasets, Gene Expression Omnibus:
NCBI, Bethesda, MD USA - NCBI, National Center fo Biotechnology Information:
Bethesda, MD USA - PubMed, Biomedical literature full-text archive:
PubMed, NCBI, Bethesda, MD USA - PubMed Central, Biomedical literature citations and abstracts:
PubMed, NCBI, Bethesda, MD USA - SRA, Sequence Read Archive:
SRA, NCBI, Bethesda, MD, USA - UCSC Genome Browser Gateway - D. melanogaster:
UCSC Genome Browser, UC Santa Cruz, USA
Data and Metadata for Drosophila Genomes
- D. albomicans Genome:
D. albomicans Organism Overview, NCBI, USA
D. albomicans Genome Assembly Report, ENA, UK - D. ananassae Genome:
D. ananassae Organism Overview, NCBI, USA
D. ananassae Genome Assembly Report, ENA, UK - D. biarmipes Genome:
D. biarmipes Organism Overview, NCBI, USA
D. biarmipes Genome Assembly Report, ENA, UK - D. bipectinata Genome:
D. bipectinata Organism Overview, NCBI, USA
D. bipectinata Genome Assembly Report, ENA, UK - D. erecta Genome:
D. erecta Organism Overview, NCBI, USA
D. erecta Genome Assembly Report, ENA, UK - D. elegans Genome:
D. elegans Organism Overview, NCBI, USA
D. elegans Genome Assembly Report, ENA, UK - D. eugracilis Genome:
D. eugracilis Organism Overview, NCBI, USA
D. eugracilis Genome Assembly Report, ENA, UK - D. ficusphila Genome:
D. ficusphila Organism Overview, NCBI, USA
D. ficusphila Genome Assembly Report, ENA, UK - D. grimshawi Genome:
D. grimshawi Organism Overview, NCBI, USA
D. grimshawi Genome Assembly Report, ENA, UK - D. kikkawai Genome:
D. kikkawai Organism Overview, NCBI, USA
D. kikkawai Genome Assembly Report, ENA, UK - D. melanogaster Genome:
D. melanogaster Organism Overview, NCBI, USA
D. melanogaster Genome Assembly Report, ENA, UK - D. miranda Genome:
D. miranda Organism Overview, NCBI, USA
D. miranda Genome Assembly Report, ENA, UK - D. mojavensis Genome:
D. mojavensis Organism Overview, NCBI, USA
D. mojavensis Genome Assembly Report, ENA, UK - D. persimilis Genome:
D. persimilis Organism Overview, NCBI, USA
D. persimilis Genome Assembly Report, ENA, UK - D. pseudoobscura Genome:
D. pseudoobscura Organism Overview, NCBI, USA
D. pseudoobscura Genome Assembly Report, ENA, UK - D. rhopaloa Genome:
D. rhopaloa Organism Overview, NCBI, USA
D. rhopaloa Genome Assembly Report, ENA, UK - D. sechellia Genome:
D. sechellia Organism Overview, NCBI, USA
D. sechellia Genome Assembly Report, ENA, UK - D. simulans Genome:
D. simulans Organism Overview, NCBI, USA
D. simulans Genome Assembly Report, ENA, UK - D. suzukii Genome:
D. suzukii Organism Overview, NCBI, USA
D. suzukii Genome Assembly Report, ENA, UK - D. takahashii Genome:
D. takahashii Organism Overview, NCBI, USA
D. takahashii Genome Assembly Report, ENA, UK - D. virilis Genome:
D. virilis Organism Overview, NCBI, USA
D. virilis Genome Assembly Report, ENA, UK - D. willistoni Genome:
D. willistoni Organism Overview, NCBI, USA
D. willistoni Genome Assembly Report, ENA, UK - D. yakuba Genome:
D. yakuba Organism Overview, NCBI, USA
D. yakuba Genome Assembly Report, ENA, UK
Genome sequencing projects
- D. pseudoobscura genome project:
D. pseudoobscura Human Genome Sequencing Center, Baylor College of Medicine, USA - D. simulans genome project:
D. simulans White 501 Genome Sequencing Center, Washington University, USA - D. yakuba genome project:
D. yakuba Genome Sequencing Center, Washington University, USA - D. simulans and yakuba sequencing projects:
DPGP, University of California, Davis, USA
Gene Expression Databases and Tools
- BDGP in situ, Patterns of gene expression in Drosophila embryogenesis:
Gene expression database, BDGP, UC Berkeley, USA - BDTNP, A cellular resolution 3D gene expression and morphology Atlas of the blastoderm.
Berkeley Drosophila Transcription Network Project, University of California, Berkeley, USA - FlAnnotator, Annotation of Gene Expression:
FlyAnnotator - 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 - flytrap, a database of P{GAL4} enhancer traps and their expression in brains:
flytrap, University of Edinburgh, UK - GEO Profiles, Gene Expression Omnibus:
GEO, NCBI, Bethesda, MD USA
General Bioinformatics Tools
- Bioconductor, Open Source Software for Bioinformatics:
Fred Hutchinson Cancer Research Center, Seattle, USA - BioMart, Data Warehouse:
BioMart, EMBL-EBI, OICR, SRSI - Cytoscape - Network Data Integration, Analysis, and Visualization in a Box:
Cytoscape - DAVID (NIH) - Database for Annotation , Visualization and Integrated Discovery:
DAVID, NIH, Bethesda, MD, USA - FlyMine, an integrated database for Drosophila &: Anopheles genomics:
University of Cambridge, United Kingdom - Galaxy: Open Source Bioinformatics Tools:
Galaxy, Penn State, PA USA and Emory University, GA USA - GSEA, Gene Set Enrichment Analysis:
GSEA, Broad Institute, Cambridge, MA, USA - GOrilla - Gene Ontology enRIchment and anaLysis and viuaLizAtion tool:
GOrilla
Interaction and Pathway 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 - IntAct, Molecular Interaction Database:
IntAct, EMBL-EBI, Hinxton, UK - KEGG - Kyoto Encyclopedia of Genes and Genomes:
KEGG, Kyoto, Japan - Reactome Pathway Database:
Reactome, OICR, Ontario, Canada, EMBL-EBI, UK, NYU Medical Center, NY, USA - STRING, Known and Predicted Protein-Protein Interactions
STRING
Miscellaneous
- Bloomington Stock Center, Drosophila and Human Disease page:
Bloomington Stock Center, Bloomington, IN, USA - Drosophila Information Service:
DIS, Norman, Oklahoma, USA - FlyTree, the Drosophila Researcher Genealogy has been incorporated into the Academic Tree Project:
FlyTree, USA - GenAge - The ageing Gene Database:
GeneAge - Homophila, Human Disease to Drosophila Gene Database:
Homophila, San Diego, 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 - 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 - 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. - The WWW Virtual Library--Drosophila:
Drosophila Virtual Library
Phylogenetic Comparison Tools
- Assembly/Alignment/Annotation of 12 related Drosophila species:
Assembly/Alignment/Annotation, LBNL, USA - DIOPT, DRSC Integrative Ortholog Prediction Tool:
DRSC, Harvard Medical School, Boston, MA, USA - EvoPrinter, Identification of Evolutionarily Resilient DNA Sequences
NINDS, NIH, Bethesda MD, USA - InParanoid, Eukaryotic Ortholog Groups:
InParanoid, Karolinska Institute, Sweden - MANTiS a phylogenetic framework for multi-species genome comparisons:
MANTiS, Université Libre de Bruxelles, Belgium - NCBI HomoloGene - automated system fo constructing putative homology groups:
NCBI, Bethesda, MA, USA - OrthoDB, the Hierarchical Catalog of Orthologs:
http://orthodb.org/orthodb7 OrthoDB, University of Geneva, Switzerland] - Vista Tools - Whole Genome Comparative Analysis of the D. melanogaster (CAF1) Genome:
Whole Genome Comparative Analysis of the D. melanogaster (CAF1) Genome, LBNL, USA
Population Biology and Polymorphism Resources
- BDGP Single Nucleotide Polymorphism (SNP) Project:
Berkeley Drosophila Genome Project, University of California, Berkeley, USA - Drosophila Polymorphism Database:
Drosophila Polymorphism Database, Univ. Autònoma de Barcelona, Spain - DPGP, Drosophila Population Genomics Project:
DPGP, University of California, Davis, USA - DSPR, Drosophila Synthetic Population Resource:
DSPR, University of Kansas and UC Irvine, USA - FlySNP Project:
FlySNP, Austrian Academy of Sciences, Austria
Protein Analysis
- CluSTr protein sequence similarity analysis of Drosophila:
CluSTr proteome analysis, EBI, UK - GPCRDB, information system for G protein-coupled receptors (GPCRs):
GPCRDB, The GPCRDB (G Protein-Coupled Receptor Data Base) partnership - InterPro protein domain analysis of Drosophila:
InterPro: protein sequence analysis & classification, EBI, UK - MEROPS, an information resource for peptidases:
MEROPS, The Sanger Institute, Cambridge, UK - 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 - SMART, Simple Modular Architecture Research Tool:
SMART, Protein Domain Analysis, EMBL, Heidleberg - UniProtKB, a comprehensive catalog of information on proteins:
UniProtKB, The UniProt Consortium
RNA and RNAi Databases and Tools
- DRSC, Drosophila RNAi Screening Center:
DRSC, Harvard Medical School, Boston, MA, USA - GenomeRNAi, Heidelberg, a database of RNA interference (RNAi) screens in cultured Drosophila cells:
GenomeRNAi, DKFZ, Heidelberg, Germany - miRBase, microRNA data:
miRBase, The Sanger Institute, Cambridge, UK - miRNA, Target Gene Prediction:
miRNA - Target Prediction, EMBL, Heidelberg, Germany - miRNA_Targets:
miRNA targets on full length mRNAs, Deakin University, Victoria, Australia - Rfam, RNA families database of alignments and CMs:
Rfam, the Sanger Institute, Cambridge, UK and Janelia Farm, Ashburn, VA, USA - TargetScanFly, Prediction of microRNA targets:
TargetScanFly, Whitehead Institute and MIT Dept. of Biology, USA - UP-TORR Fly, a tool for identifying updated targets of RNAi reagents:
Updated Targets of RNAi Reagents, DRSC, Harvard Medical School, Boston, MA,USA
Sequence Analysis
- 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 - MEME Suite - Motif-based Sequence Analysis Tools:
MEME - RepeatMasker:
RepeatMasker - Splice Site Prediction for Drosophila:
Splice Site Prediction, Berkeley Drosophila Genome Project, University of California, Berkeley, USA - Web Apollo, a collaborative genomic annotation editor:
Web Apollo, LBL, Berkeley, USA
Taxonomy
- Drosophilidae Taxonomic Database:
Drosophilidae Taxonomic Database, Japan - Drosophilidae Taxonomy - Collection of Papers:
Japan Drosophila Database (JDD) on Taxonomy, Japan - FlyPhenomics, phenotypic differences between species of the D. melanogaster subgroup:
FlyPhenomics, Paris, France - GEO, NCBI's Gene Expression Omnibus:
GEO, NCBI, Bethesda, MD USA - TaxoDros, the database on Taxonomy of Drosophilidae:
TaxoDros, University of Zurich, Switzerland - Taxonomy, NCBI Taxonomy Database:
NCBI, Bethesda, MD USA
Transcription Regulation Databases
- BDTNP, ChIP/chip in vivo DNA binding data:
Berkeley Drosophila Transcription Network Project, University of California, Berkeley, USA - cis-analyst, to search the Drosophila genome for clusters of binding sites:
cis-analyst, USA - DBD: Transcription factor prediction database:
DBD - DNase I Footprint Database::
University of Manchester Bioinformatics Resources, University of Manchester, UK - EPD, the Eukaryotic Promoter Database:
EPD, Epalinges s/Lausanne, Switzerland - Fly Factor Survey - Database of Drosophila TF DNA-binding Specificitiies:
FLy Factor Survey, UMass Medical School, Worcester, MA, USA - OnTheFly, Database of Drosophila Transcription Factors and Transcription Factor Binding Sites
Columbia University, USA - 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 - REDfly, Regulatory Element Database for Drosophila:
REDfly, University at Buffalo, New York, USA - The Drosophila Transcription Factor Database:
FlyTF.org, MRC Cambridge, UK - TRANSFAC, A database of transcription factors and their binding sites:
TRANSFAC, Braunschweig, Germany