Difference between revisions of "FlyBase:Drosophila Online Resources"
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=Orthologs= | =Orthologs= | ||
| − | * <b>DIOPT</b>, DRSC Integrative Ortholog Prediction Tool | + | * <b>DIOPT</b>, DRSC Integrative Ortholog Prediction Tool<br />[http://www.flyrnai.org/cgi-bin/DRSC_orthologs.pl DRSC, Harvard Medical School, Boston, MA, USA] |
| − | * <b>DIOPT-DIST: DIOPT Diseases and Traits</b>, DRSC Disease Gene Query Tool:<br />[http://www.flyrnai.org/cgi-bin/DRSC_DG_query.pl | + | * <b>DIOPT-DIST: DIOPT Diseases and Traits</b>, DRSC Disease Gene Query Tool:<br />[http://www.flyrnai.org/cgi-bin/DRSC_DG_query.pl DRSC, Harvard Medical School, Boston, MA, USA] |
| − | * <b>OrthoDB</b>, The Hierarchical Catalog of Orthologs | + | * <b>OrthoDB</b>, The Hierarchical Catalog of Orthologs<br />[http://orthodb.org/ Zdobnov Computational Evolutionary Genomics group, University of Geneva, Geneva, Switzerland] |
| + | * <b>Compara</b>, Ensembl Compara provides cross-species resources and analyses, at both the sequence level and the gene level.<br />[http://useast.ensembl.org/info/genome/compara/index.html?redirect=no Ensembl, Hinxton, UK] | ||
| + | * <b>Homologene</b>, An automated system for constructing putative homology groups from the complete gene sets of a wide range of eukaryotic species.<br />[http://www.ncbi.nlm.nih.gov/homologene NCBI, Bethesda, MD, USA] | ||
| + | * <b>Inparanoid</b>, InParanoid: ortholog groups with inparalogs<br />[http://inparanoid.sbc.su.se/cgi-bin/index.cgi Stockholm Bioinformatics Centre, Stockholm, Sweden] | ||
| + | * <b>Isobase</b>, A Database of Functionally Related Orthologs, which incorporates PPI network data in addition to sequence similarity.<br />[http://groups.csail.mit.edu/cb/mna/isobase/ MIT, Cambridge, MA, USA] | ||
| + | * <b>OMA Browser</b>, The OMA (“Orthologous MAtrix”) project is a method and database for the inference of orthologs among complete genomes.<br />[http://omabrowser.org/oma/home/ Nucl. Acids Res. 43 (D1): D240-D249. doi: 10.1093/nar/gku1158] | ||
| + | * <b>OrthoMCL</b>, Ortholog Groups of Protein Sequences<br />[http://www.orthomcl.org/orthomcl/ EuPathDB] | ||
| + | * <b>PhylomeDB</b>, PhylomeDB is a public database for complete catalogs of gene phylogenies (phylomes)<br />[http://phylomedb.org/ Comparative Genomics Groups at CRB, Barcelona, Spain] | ||
| + | * <b>Roundup</b>, A large-scale orthology database using the Reciprocal Smallest Distance (RSD) algorithm.<br />[http://wall-lab.stanford.edu/projects/roundup/ Wall lab, Stanford University, Palo Alto, CA, USA] | ||
| + | * <b>TreeFam</b>, A database composed of phylogenetic trees inferred from animal genomes. It provides orthology/parology predictions as well the evolutionary history of genes.<br />[http://www.treefam.org/ EMBL-EBI, Hinxton, UK] | ||
=Phylogenetic Comparison Tools= | =Phylogenetic Comparison Tools= | ||
Revision as of 20:10, 10 December 2015
Atlases, Images and Videos
- Atlas of Drosophila Development, An Atlas following the main events of embryogenesis and post-embryonic development:
Volker Hartenstein and Interactive Fly, Bethesda, MD, USA - BDTNP, A cellular resolution 3D gene expression and morphology Atlas of the blastoderm:
Berkeley Drosophila Transcription Network Project, University of California, Berkeley, USA - BrainTrap, a collection of 3D confocal datasets taken from EYFP expressing protein trap Drosophila lines from the Cambridge Protein Trap project:
Armstrong Lab, University of Edinburgh, Edinburgh, UK - CSIRO Anatomical Atlas of Flies:
CSIRO Entomology, Australia - Electron micrograph maps of D. 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 - FlyGut, An interactive Database that aims to provide a comprehensive atlas of the Drosophila melanogaster adult midgut (see also, FlyGut-seq):
Buchon Lab, Cornell University, Ithaca, NY, USA & Lemaitre Lab, EPFL, Lausanne, Switzerland - 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 - Interactive Maps: four maps displaying markers and lineages of D. melanogaster neuroblasts, glial cells, and interneurons:
Interactive Maps, Institut fur Genetik, Johannes Gutenberg University, Mainz, Germany - Jove, videos of experimental techniques:
Jove, Journal of Visualized Experiments, USA - Learning to Fly, a poster describing marker phenotypes in the fruit fly:
Genesis (Journal), Wiley Online Library - PeptideAtlas, a multi-organism, publicly accessible compendium of peptides identified in a large set of tandem mass spectrometry proteomics experiments:
Seattle Proteome Center, Seattle, Washington, 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 - CCTop CRISPR/Cas9 optimum target finder:
Center for Organismal Studies, Heidelberg University, Heidelberg, DE - CHOPCHOP CRISPR/Cas9 target online predictor, mammalian and other major model organisms including fly:
Schier Lab, Harvard University, Cambridge, MA, Church Lab, Harvard Medical School, Boston, MA, USA - CRISPOR Model organism gRNA design tool:
TEFOR, Gif-sur-Yvette, France - CRISPR/Cas Web Resources Web Resources for design and planning of CRISPR/Cas9 studies:
IGTRCN, Insect Genetic Technologies Research Coordination Network, University of Maryland, Rockville, MD, USA - CRISPR-ERA A Fast and Comprehensive Guide RNA Design Tool for Genome Editing, Repression and Activation:
Lei Stanley Qi Lab and Xiaowo Wang Lab, Stanford University, Palo Alto, CA, USA - CRISPR Genome Engineering Resources CRISPR Design Tool:
Zhang Lab, MIT, Boston, MA, USA - CRISPR fly design -- reagents, protocols, and results from fly CRISPR/Cas experiments:
Bullolk Lab, MRC Laboratory of Molecular Biology, Cambridge, UK - CRISPRscan Novel scoring algorithm for selecting sgRNAs
Giraldez Lab, Yale University, New Haven, CT, USA - DRSC CRISPR Efficiency Tool for Assessment of Designs:
DRSC, Harvard Medical School, Boston, MA, USA - DRSC Finding CRISPRs, Drosophila CRISPR gRNA design search tool:
DRSC, Harvard Medical School, 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 - flyCRISPR, Resource Site:
O'Connor-Giles, Wildonger, and Harrison Labs, University of Wisconsin-Madison, WI, USA - flyCRISPR, Optimal Target Finder:
O'Connor-Giles Lab, University of Wisconsin-Madison, 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 - SIFTED, Specificity Inference for TAL Effector Design:
Bulyk Lab, Harvard Medical School, Boston, MA, USA - 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 - NCBI Map Viewer, A genome view of Drosophila melanogaster:
NCBI, 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
- DroSpeGe, a view of Drosophila genome data, with genome maps and BLAST sequence search, for 12 species:
Genome Informatics Lab, Indiana University, Bloomington, Indiana, USA - List of Drosophila reference genome assemblies at FlyBase, NCBI and UCSC. File:DrosophilaGenomeAssemblies.xls (spreadsheet) Updated June 17, 2015
- D. albomicans Genome:
D. albomicans Organism Overview, NCBI, USA
D. albomicans Genome Assembly Report, NCBI, USA
D. albomicans Genome Assembly Report, ENA, UK - D. ananassae Genome:
D. ananassae Organism Overview, NCBI, USA
D. ananassae Genome Assembly Report, NCBI, USA
D. ananassae Genome Assembly Report, ENA, UK - D. biarmipes Genome:
D. biarmipes Organism Overview, NCBI, USA
D. biarmipes Genome Assembly Report, NCBI, USA
D. biarmipes Genome Assembly Report, ENA, UK - D. bipectinata Genome:
D. bipectinata Organism Overview, NCBI, USA
D. bipectinata Genome Assembly Report, NCBI, USA
D. bipectinata Genome Assembly Report, ENA, UK - D. erecta Genome:
D. erecta Organism Overview, NCBI, USA
D. erecta Genome Assembly Report, NCBI, USA
D. erecta Genome Assembly Report, ENA, UK - D. elegans Genome:
D. elegans Organism Overview, NCBI, USA
D. elegans Genome Assembly Report, NCBI, USA
D. elegans Genome Assembly Report, ENA, UK - D. eugracilis Genome:
D. eugracilis Organism Overview, NCBI, USA
D. eugracilis Genome Assembly Report, NCBI, USA
D. eugracilis Genome Assembly Report, ENA, UK - D. ficusphila Genome:
D. ficusphila Organism Overview, NCBI, USA
D. ficusphila Genome Assembly Report, NCBI, USA
D. ficusphila Genome Assembly Report, ENA, UK - D. grimshawi Genome:
D. grimshawi Organism Overview, NCBI, USA
D. grimshawi Genome Assembly Report, NCBI, USA
D. grimshawi Genome Assembly Report, ENA, UK - D. kikkawai Genome:
D. kikkawai Organism Overview, NCBI, USA
D. kikkawai Genome Assembly Report, NCBI, USA
D. kikkawai Genome Assembly Report, ENA, UK - D. melanogaster Genome:
D. melanogaster Organism Overview, NCBI, USA
D. melanogaster Genome Assembly Report, NCBI, USA
D. melanogaster Genome Assembly Report, ENA, UK - D. miranda Genome:
D. miranda Organism Overview, NCBI, USA
D. miranda Genome Assembly Report, NCBI, USA
D. miranda Genome Assembly Report, ENA, UK - D. mojavensis Genome:
D. mojavensis Organism Overview, NCBI, USA
D. mojavensis Genome Assembly Report, NCBI, USA
D. mojavensis Genome Assembly Report, ENA, UK - D. persimilis Genome:
D. persimilis Organism Overview, NCBI, USA
D. persimilis Genome Assembly Report, NCBI, USA
D. persimilis Genome Assembly Report, ENA, UK - D. pseudoobscura Genome:
D. pseudoobscura Organism Overview, NCBI, USA
D. pseudoobscura Genome Assembly Report, NCBI, USA
D. pseudoobscura Genome Assembly Report, ENA, UK - D. rhopaloa Genome:
D. rhopaloa Organism Overview, NCBI, USA
D. rhopaloa Genome Assembly Report, NCBI, USA
D. rhopaloa Genome Assembly Report, ENA, UK - D. sechellia Genome:
D. sechellia Organism Overview, NCBI, USA
D. sechellia Genome Assembly Report, NCBI, USA
D. sechellia Genome Assembly Report, ENA, UK - D. simulans Genome:
D. simulans Organism Overview, NCBI, USA
D. simulans Genome Assembly Report, NCBI, USA
D. simulans Genome Assembly Report, ENA, UK - D. suzukii Genome:
D. suzukii Organism Overview, NCBI, USA
D. suzukii Genome Assembly Report, NCBI, USA
D. suzukii Genome Assembly Report, ENA, UK - D. takahashii Genome:
D. takahashii Organism Overview, NCBI, USA
D. takahashii Genome Assembly Report, NCBI, USA
D. takahashii Genome Assembly Report, ENA, UK - D. virilis Genome:
D. virilis Organism Overview, NCBI, USA
D. virilis Genome Assembly Report, NCBI, USA
D. virilis Genome Assembly Report, ENA, UK - D. willistoni Genome:
D. willistoni Organism Overview, NCBI, USA
D. willistoni Genome Assembly Report, NCBI, USA
D. willistoni Genome Assembly Report, ENA, UK - D. yakuba Genome:
D. yakuba Organism Overview, NCBI, USA
D. yakuba Genome Assembly Report, NCBI, USA
D. yakuba Genome Assembly Report, ENA, UK]
Gene Expression Databases and Tools
- BDGP in situ, Patterns of gene expression in Drosophila embryogenesis:
Gene expression database, BDGP, University of California, 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 - cisPatterns, A database of over 100 Drosophila GAL4-driver lines regulated by single cis-regulatory enhancers:
Jermaine Ross and the Odenwald Lab, NINDS, NIH, Bethesda MD, USA - DGRC, Cell Line Expression tool (based on modENCODE data):
DGRC, University of Indiana, Bloomington, IN, USA - DRSC, Cell Line Expression tool (based on modENCODE data):
DRSC, Harvard Medical School, 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 - FlyGut-seq, a transcriptomic resource that complements the original Flygut website:
Buchon Lab, Cornell University, Ithaca, NY, 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 - RNAMiner, A Bioinformatics Protocol for Mining Large RNA-Seq Transcriptomics Data:
Cheng Lab, University of Missouri, Mizzou, Columbia, MO, USA
Gene Groups
- FlyBase Gene Group Reports:
FlyBase Consortium - GLAD, an Online Database of Gene List Annotations for Drosophila:
DRSC, Harvard Medical School, Boston, MA, 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 - DNA & Protein Work List, A list of tools aggregated by the Prokop Lab:
http://www.prokop.co.uk/Links/tools.html - FlyMine, an Integrated Database for Drosophila and Anopheles Genomics:
University of Cambridge, United Kingdom - FlyNet, a network prioritization server for Drosophila melanogaster biology:
NetBioLab, Yonsei University, Seoul, Korea - 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
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
Human Disease: Drosophila Models and Orthologous Genes
- FlyBase Human Disease Model Reports:
FlyBase Consortium - 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 - Drosophila as a Model for Human Diseases:
Interactive Fly, Bethesda, MD, USA - Drosophila Models of Human Disease, a blog by Stephanie Mohr and Annette Parks:
flydiseasemodels.blogspot.com/ - FlyNet Human Disease Prioritization:
NetBioLab, Yonsei University, Seoul, Korea - 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 - DAPPER, database for protein-protein interactions:
DAPPER, University of Cambridge, Cambridge, UK - 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 - FlyNet Gene Prioritization:
NetBioLab, Yonsei University, Seoul, Korea - 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
Laboratory Resources
- Laboratory Manual of Drosophila:
PDF, Chippindale, A. et al., Department of Ecology & Evolutionary Biology, University of California, Irvine, USA
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, DRSC, Harvard Medical School, Boston, MA, USA - miRBase, microRNA data:
miRBase, University of Manchester, UK
- NOTE - mirBase Release 21 (June 2014) uses old reference genome assemblies for D. melanogaster (Dmel_Release_5), D. simulans (Dsim_Release_1) and D. pseudoobscura (Dpse_Release_2). Linkouts from D. melanogaster miRNA genes to the Ensembl Genome browser (which displays Dmel_Release_6) will point to the old "Release_5" coordinates, which will be off the mark for many genes, especially those on X, 2R, 3R and 4 chromosomes.
- 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]
Miscellaneous
- Bionet Archives, a collection of bionet USENET newsgroups and parallel e-mail lists regarding Drosophila:
Genome Informatics Lab, Indiana University, Bloomington, Indiana, USA - DOR, Database of Olfactory Receptors:
DOR, NCBS, Bangalore, India, AIST, Tokyo, Japan - Drosophila App, A mobile application developed by Genesee for use in fly research:
iTunes | Android - Drosophila Information Service:
DIS, Norman, Oklahoma, USA - Fly Labs and References, a large list of fly labs and recent publications:
Interactive Fly, Bethesda, MD, 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, Harvard Medical School, Boston, MA, USA - IGTRCN, Insect Genetic Technologies Research Coordination Network:
IGTRCN, University of Maryland, Rockville, MD, 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 - Manchester Fly Facility, Outreach resources - A compendium of information on Drosophila melanogaster as a model organism:
University of Manchester, Manchester, 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 - Multiplex Fluorescent mRNA In Situ Hybridization, information on how to perform multiplex fluorescent mRNA in situ hybridization on Drosophila embryos:
Bier and McGinnis Labs, UCSD, San Diego, California, 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. - What's hot today: Current papers in developmental biology and gene function:
Interactive Fly, Bethesda, MD, USA - The WWW Virtual Library--Drosophila:
Drosophila Virtual Library
Ontology Resources
- The OBO Foundry, an ontology registry:
OboFoundry - Ontobee, an ontologies browser:
Ontobee, He Group, University of Michigan Medical School, Ann Arbor, Michigan, USA - BioPortal, a biomedical ontologies repository and browser:
BioPortal, The National Center for Biomedical Ontology, USA - Ontology Lookup Service, an ontologies browser:
Ontology Lookup Service, EMBL-EBI, Hinxton, UK - QuickGO, a browser for Gene Ontology terms and annotations:
QuickGO, EMBL-EBI, Hinxton, UK - AmiGO 2, tools for searching and browsing the Gene Ontology database:
AmiGO 2, Berkeley Bioinformatics Open-source Projects, USA - Gene Ontology Consortium
Gene Ontology Consortium - OboEdit, browser for OBO ontologies:
OboEdit - Protege, browser for OWL ontologies:
Protege, Stanford Center for Biomedical Informatics Research, Stanford University School of Medicine, USA - Disease Ontology, ontology of disease terms:
Disease Ontology
Orthologs
- DIOPT, DRSC Integrative Ortholog Prediction Tool
DRSC, Harvard Medical School, Boston, MA, USA - DIOPT-DIST: DIOPT Diseases and Traits, DRSC Disease Gene Query Tool:
DRSC, Harvard Medical School, Boston, MA, USA - OrthoDB, The Hierarchical Catalog of Orthologs
Zdobnov Computational Evolutionary Genomics group, University of Geneva, Geneva, Switzerland - Compara, Ensembl Compara provides cross-species resources and analyses, at both the sequence level and the gene level.
Ensembl, Hinxton, UK - Homologene, An automated system for constructing putative homology groups from the complete gene sets of a wide range of eukaryotic species.
NCBI, Bethesda, MD, USA - Inparanoid, InParanoid: ortholog groups with inparalogs
Stockholm Bioinformatics Centre, Stockholm, Sweden - Isobase, A Database of Functionally Related Orthologs, which incorporates PPI network data in addition to sequence similarity.
MIT, Cambridge, MA, USA - OMA Browser, The OMA (“Orthologous MAtrix”) project is a method and database for the inference of orthologs among complete genomes.
Nucl. Acids Res. 43 (D1): D240-D249. doi: 10.1093/nar/gku1158 - OrthoMCL, Ortholog Groups of Protein Sequences
EuPathDB - PhylomeDB, PhylomeDB is a public database for complete catalogs of gene phylogenies (phylomes)
Comparative Genomics Groups at CRB, Barcelona, Spain - Roundup, A large-scale orthology database using the Reciprocal Smallest Distance (RSD) algorithm.
Wall lab, Stanford University, Palo Alto, CA, USA - TreeFam, A database composed of phylogenetic trees inferred from animal genomes. It provides orthology/parology predictions as well the evolutionary history of genes.
EMBL-EBI, Hinxton, UK
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 Genetics Reference Panel:
DGRP, Baylor College of Medicine, Houston, TX and NC State University, Raleigh, NC USA - Drosophila Genetics Reference Panel 2:
DGRP2, NC State University, Raleigh, NC and Baylor College of Medicine, Houston, TX, USA - Drosophila Polymorphism Database:
DGRP2, 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 - FlyVar Project: A Database of Drosophila Genetics Variations
FlyVar, Fudan University, Shanghai, China and Baylor College of Medicine, Houston, TX, USA
Protein Analysis
- ExPASy, the SIB Bioinformatics Resource Portal which provides access to scientific databases and software tools in different areas of life sciences:
SIB Swiss Institute of Bioinformatics, Genève, Switzerland - 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 - PhospoPep, interactive interrogation of MS-derived phosphorylation data from 4 different organisms:
Institute for Systems Biology, Seattle, Washington, USA - ProteinProspector, a proteomics tools for mining sequence databases in conjunction with Mass Spectrometry experiments:
UCSF Mass Spectrometry Facility, San Francisco, California, USA - SMART, Simple Modular Architecture Research Tool:
SMART, Protein Domain Analysis, EMBL, Heidleberg - UniProtKB, a comprehensive catalog of information on proteins:
UniProtKB, The UniProt Consortium
Public Education
- About the history of Drosophila research, An extensive collection of media pertaining to the history of fruit fly research:
Manchester Fly Facility, University of Manchester, UK - droso4schools, An online resource for school lessons using the fruit fly Drosophila:
Manchester Fly Facility, University of Manchester, UK - Drosophila & Computer Programming Game, A scratch computer game based on the Drosophila life cycle:
Manchester Fly Facility, University of Manchester, UK - Genetic Portraits, An overview of commonly used model organisms in genetic research:
McGraw-Hill Higher Education - Fly on the Wall, a blog by Bethany Christmann regarding fruit flies and research:
Griffith Lab, Brandeis University, Waltham, MA, USA - FlyMove, an Image, Movie and Interactive Shockwave Resource:
FlyMove, Muenster, Germany - Manchester Fly Facility Public Resource Page:
Manchester Fly Facility, University of Manchester, UK
RNAi
- DRSC, Drosophila RNAi Screening Center:
DRSC, Harvard Medical School, Boston, MA, USA - Search by gene(s) to find hits in DRSC screens:
DRSC, Harvard Medical School, Boston, MA, USA - FlyRNAi blog, a DRSC resource concerning RNAi, cell-based assays, Drosophila cell culture, high-throughput screening, & fly biology:
flyrnai.blogspot.com - Fosmid rescue analysis tool for identification of fosmids appropriate for cross-species rescue of RNAi:
DRSC, Harvard Medical School, Boston, MA, USA - GenomeRNAi, Heidelberg, a database of RNA interference (RNAi) screens:
GenomeRNAi, DKFZ, Heidelberg, Germany - GESS, off-target RNAi prediction:
DRSC, Harvard Medical School, Boston, MA, USA - Predicted Off-Target Free Sequence Regions:
DRSC, Harvard Medical School, Boston, MA, USA - RNAiCut, Automated Detection of Significant Genes from Functional Genomic Screens:
Berger Lab, MIT, 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 - Tsinghua Fly Center, Transgenic RNAi lines:
Center of Biomedical Analysis, Tsinghua University, Beijing, China - 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
- DCPD -- Drosophila Core Promoter Database, A list of 205 Drosophila melanogaster core promoters aligned by their empirically determined transcription start site:
Kadonaga Lab, UCSD, San Diego, California, USA - EvoPrinterHD, A "High Definition" view of conserved DNA:
NINDS, NIH, Bethesda, MD, 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 - HRMA -- High Resolution Melt Analysis:
HRMA, DRSC, Harvard Medical School, Boston, MA, 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, Searching the Drosophila genome for clusters of binding sites:
cis-analyst, Berkeley, USA - CORE, A database utilizing the ElemeNT algorithm (see below) to annotate individual Drosophila observed TSS (using either CAGE or RNAseq data) for the presence of the various core promoter elements:
Juven-Gershon Lab, Bar-Ilan University, Ramat-Gan, Israel - DBD, Transcription factor prediction database:
DBD, MRC, Cambridge, UK - ElemeNT, An interactive tool for rapid and convenient detection of core promoter elements within a given sequence, implemented in Perl programming language:
Juven-Gershon Lab, Bar-Ilan University, Ramat-Gan, Israel - FlyReg, 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
Suggest a tool or resource
- Please contact Flybase to suggest a tool or resource for the list.