Difference between revisions of "FlyBase:Drosophila Online Resources"
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=Interaction and Pathway Databases= | =Interaction and Pathway Databases= | ||
* BioGRID, The General Repository for Interaction Datasets:<br />[http://www.thebiogrid.org/index.php BioGRID, Mount Sinai Hospital, Toronto, Canada] | * BioGRID, The General Repository for Interaction Datasets:<br />[http://www.thebiogrid.org/index.php BioGRID, Mount Sinai Hospital, Toronto, Canada] | ||
| + | * COMPLEAT, protein COMPLex Enrichment Analysis Tool:<br />[http://www.flyrnai.org/compleat/ COMPLEAT, DRSC, Harvard Medical School, Boston, MA, USA] | ||
* DPiM, Drosophila Protein interaction Map:<br />[https://interfly.med.harvard.edu/ DPiM, Harvard University Medical School, Boston, MA, USA] | * DPiM, Drosophila Protein interaction Map:<br />[https://interfly.med.harvard.edu/ DPiM, Harvard University Medical School, Boston, MA, USA] | ||
* DroID, Drosophila Interactions Database:<br />[http://www.droidb.org/ Drosophila Interaction Database, Detroit, USA] | * DroID, Drosophila Interactions Database:<br />[http://www.droidb.org/ Drosophila Interaction Database, Detroit, USA] | ||
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* KEGG - Kyoto Encyclopedia of Genes and Genomes:<br />[http://www.genome.jp/kegg KEGG, Kyoto, Japan] | * KEGG - Kyoto Encyclopedia of Genes and Genomes:<br />[http://www.genome.jp/kegg KEGG, Kyoto, Japan] | ||
* Reactome Pathway Database:<br />[http://www.reactome.org/ Reactome, OICR, Ontario, Canada, EMBL-EBI, UK, NYU Medical Center, NY, USA] | * Reactome Pathway Database:<br />[http://www.reactome.org/ Reactome, OICR, Ontario, Canada, EMBL-EBI, UK, NYU Medical Center, NY, USA] | ||
| + | * SignedPPI, Searchable Database of Known and Predicted Protein-protein Interactions:<br />[http://www.flyrnai.org/SignedPPI/ DRSC, Harvard Medical School, Boston, MA, USA] | ||
* STRING, Known and Predicted Protein-Protein Interactions<br />[http://string-db.org/ STRING, SIB, Switzerland CPR, Denmark, and EMBL, Heidelberg, Germany] | * STRING, Known and Predicted Protein-Protein Interactions<br />[http://string-db.org/ STRING, SIB, Switzerland CPR, Denmark, and EMBL, Heidelberg, Germany] | ||
Revision as of 20:14, 19 December 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, Kyoto Institute of Technology, Kyoto, 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
CRISPRs and TALENs
- Cas9 Design:
Center for Bioinformatics, Peking University, Peking, China - CRISPR Efficiency Tool for Assessment of Designs:
DRSC, Boston, MA, USA - CRISPR Genome Engineering Resources:
Zhang lab, MIT, Boston, MA, USA - E-CRISP, Design of CRISPR Constructs:
DKFZ/Boutros lab, Heildelberg, Germany - E-TALEN, Design of TALEN Constructs:
DKFZ/Boutros lab, Heildelberg, Germany - Finding CRISPRs, Drosophila CRISPR gRNA design search tool:
DRSC, Boston, MA, USA - flyCRISPR, Optimal Target Finder:
O'Connor-Giles Lab, Bullock Lab, University of Wicsconsin, WI, USA - Genome Engineering by CRISPR/Cas9 in Drosophila:
NIG/FLY/Ueda lab, Mishima, Japan - Mojo Hand, A TALEN Design Tool:
Ekker lab, Mayo Clinic, Rochester, MN, USA - OXfCRISPR, Oxford Fly CRISPR Resources:
Liu lab, University of Oxford, Oxford, UK - TAL Effectors:
Zhang lab, MIT, Boston, MA, USA - TALengineering.org, A Comprehensive Resource for Engineered TAL Effector Technology:
Ekker lab, Joung Lab, MGH, Boston, USA - ZiFiT Targeter, Tool for Identifying Zinc Finger Nuclease Sites in Specific Target Sequences:
MGH and Harvard Medical School, Boston, MA
Data Repositories
- Array Express - Functional Genomics Data:
Array Express, EMBL-EBI, Hinxton, 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, Hinxton, 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 Central, 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 - DGRC, Cell Line Expression tool (based on modENCODE data):
DGRC, Bloomington, IN, USA - DRSC, Cell Line Expression tool (based on modENCODE data):
DRSC, Boston, MA, USA - FlAnnotator, Annotation of Gene Expression:
FlyAnnotator, University of Cambridge, UK - FlyAtlas2, for exploring how genes are expressed in the tissues of D. melanogaster:
FlyAtlas2, University of Glasgow, Glasgow, UK - FlyEx, a Database of Segmentation Gene Expression in Drosophila:
FlyEx, St. Petersburg State Polytechnical University, Russia - FlyExpress, an Expression Pattern Search Engine:
FlyExpress, Arizona State University, USA - Fly-FISH, A Database of Drosophila Embryo mRNA Localizaton Patterns:
Fly-FISH, University of Toronto, Toronto, Canada - 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, Cytoscape Consortium, Canada, France, and USA - DAVID (NIH) - Database for Annotation , Visualization and Integrated Discovery:
DAVID, NIH, Bethesda, MD, USA - FlyMine, an Integrated Database for Drosophila and 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, Israel
Human Disease: Drosophila Models and Orthologous Genes
- Bloomington Stock Center, Drosophila and Human Disease page:
Bloomington Stock Center, Bloomington, IN, USA - DIOPT-DIST, Disease-related Ortholog Tool:
DRSC, Harvard Medical School, Boston, MA, USA - HuDis, high confidence human disease gene - fly gene ortholog pairs:
DRSC, Harvard Medical School, Boston, MA, USA
Interaction and Pathway Databases
- BioGRID, The General Repository for Interaction Datasets:
BioGRID, Mount Sinai Hospital, Toronto, Canada - COMPLEAT, protein COMPLex Enrichment Analysis Tool:
COMPLEAT, DRSC, Harvard Medical School, Boston, MA, USA - 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 - FlyCyc - Curated Drosophila melanogaster Pathways:
FlyCyc, Harvard University, Cambridge, USA - FlyReactome - a Curated Knowledgebase of Drosophila melanogaster Pathways:
FlyReactome, University of Cambridge, Cambridge, UK - 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 - SignedPPI, Searchable Database of Known and Predicted Protein-protein Interactions:
DRSC, Harvard Medical School, Boston, MA, USA - STRING, Known and Predicted Protein-Protein Interactions
STRING, SIB, Switzerland CPR, Denmark, and EMBL, Heidelberg, Germany
Miscellaneous
- DOR, Database of Olfactory Receptors:
DOR, NCBS, Bangalore, India, AIST, Tokyo, Japan - 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:
Human Ageing Genomic Resources, Institute of Integrative Biology, Liverpool, UK - Gene Lookup, Gene and Reagent Lookup:
Gene Lookup, DRSC, Boston, MA, 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 - PhenomicDB, A Cross-species Genotype-Phenotype Resource:
Phenotype-Genotype Database, Berlin, Germany - 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
- 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, Wellcome Trust Sanger Institute, Hinxton, 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
miRNA and ncRNA Databases and Tools
- DIANA microT-CDS, MicroRNA Target Prediction:
DIANA microT-CDS, DIANA LAB, Athens, Greece - DIANA TarBase, MicroRNA Target Database:
DIANA TarBase,, DIANA LAB, Athens, Greece - MinoTar, Predict microRNA Targets in Coding Sequence:
MinoTar, DSRC, Boston, MA, USA - miRBase, microRNA data:
miRBase, University of Manchester, UK - miRNA, Target Gene Prediction:
miRNA - Target Prediction, EMBL, Heidelberg, Germany - miRNA_Targets:
miRNA targets on full length mRNAs, Deakin University, Victoria, Australia - miRTarBase, Experimentally Validated microRNA-target Interactions Database:
miRTarBase, ISBLab, Hsinchu, Taiwan - Rfam, RNA families database of alignments and CMs:
Rfam, Wellcome Trust Sanger Institute, Hinxton, UK and Janelia Farm, Ashburn, VA, USA - TargetScanFly, Prediction of microRNA targets:
TargetScanFly, Whitehead Institute and MIT Dept. of Biology, USA]
RNAi
- 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 - GESS, off-target RNAi prediction:
DRSC, Harvard Medical School, Boston, MA, USA - RSVP, RNAi STock Validation & Phenotypes:
DRSC, Harvard Medical School, Boston, MA, USA - SnapDragon, RNAi Design:
DRSC, Harvard Medical School, Boston, MA, USA - TRiP, Transgenic RNAi Project:
Transgenic RNAi Project, DRSC, Harvard Medical School, Boston, MA,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 - VDRC, Vienna Drosophila Resource Center:
Genome-wide transgenic Drosophila RNAi libraries, VDRC, Vienna, Austria
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, U. of Queensland, U. of Washington, USA, UCSD, SDSC, NBCR, CBRC, and National Center for Research Resources - RepeatMasker:
RepeatMasker Institute for Systems Biology, Seattle, WA, USA - 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 - TaxoDros, the database on Taxonomy of Drosophilidae:
TaxoDros, University of Zurich, Switzerland - Taxonomy, NCBI Taxonomy Database:
NCBI, Bethesda, MD USA
Transcription Regulation Databases and Tools
- 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, Berkeley, USA - DBD: Transcription factor prediction database:
DBD, MRC, Cambridge, UK - 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
OnTheFly, 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