Difference between revisions of "FlyBase:Drosophila Online Resources"

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=CRISPRs and TALENs=
 
=CRISPRs and TALENs=
 
* <b>Cas9 Design</b>:<br />[http://cas9.cbi.pku.edu.cn/ Center for Bioinformatics, Peking University, Peking, China]
 
* <b>Cas9 Design</b>:<br />[http://cas9.cbi.pku.edu.cn/ Center for Bioinformatics, Peking University, Peking, China]
* <b>CCTop</b> CRISPR/Cas9 target online predictor:<br />[http://crispr.cos.uni-heidelberg.de/ Center for Organismal Studies, Heidelberg University, Heidelberg, DE]
+
* <b>CCTop</b> CRISPR/Cas9 optimum target finder:<br />[http://crispr.cos.uni-heidelberg.de/ Center for Organismal Studies, Heidelberg University, Heidelberg, DE]
* <b>CRISPR Efficiency Tool for Assessment of Designs</b>:<br />[http://www.flyrnai.org/evaluateCrispr/ DRSC, Harvard Medical School, Boston, MA, USA]
+
* <b>CHOPCHOP</b> CRISPR/Cas9 target online predictor, mammalian and other major model organisms including fly:<br />[https://chopchop.rc.fas.harvard.edu/about.php/ Schier Lab, Harvard University, Cambridge, MA, Church Lab, Harvard Medical School, Boston, MA, USA]
* <b>CRISPR Genome Engineering Resources</b>:<br />[http://www.genome-engineering.org/crispr/ Zhang lab, MIT, Boston, MA, USA]
+
* <b>CRISPOR</b> Model organism gRNA design tool:<br />[http://tefor.net/crispor/crispor.cgi/ TEFOR, Gif-sur-Yvette, France]
 +
* <b>CRISPR/Cas Web Resources</b> Web Resources for design and planning of CRISPR/Cas9 studies:<br />[http://igtrcn.org/knowledgebase/crisprcas-web-resources// IGTRCN, Insect Genetic Technologies Research Coordination Network, University of Maryland, Rockville, MD, USA]
 +
* <b>CRISPR-ERA</b> A Fast and Comprehensive Guide RNA Design Tool for Genome Editing, Repression and Activation:<br />[http://crispr-era.stanford.edu// Lei Stanley Qi Lab and Xiaowo Wang Lab, Stanford University, Palo Alto, CA, USA]
 +
* <b>CRISPR Genome Engineering Resources</b> CRISPR Design Tool:<br />[http://www.genome-engineering.org/crispr/?page_id=41/  Zhang Lab, MIT, Boston, MA, USA]
 
* <b>CRISPR fly design</b> -- reagents, protocols, and results from fly CRISPR/Cas experiments:<br />[http://www.crisprflydesign.org/ Bullolk Lab, MRC Laboratory of Molecular Biology, Cambridge, UK]
 
* <b>CRISPR fly design</b> -- reagents, protocols, and results from fly CRISPR/Cas experiments:<br />[http://www.crisprflydesign.org/ Bullolk Lab, MRC Laboratory of Molecular Biology, Cambridge, UK]
 +
* <b>CRISPRscan</b> Novel scoring algorithm for selecting sgRNAs<br />[http://www.crisprscan.org// Giraldez Lab, Yale University, New Haven, CT, USA]
 +
* <b>DRSC CRISPR Efficiency Tool for Assessment of Designs</b>:<br />[http://www.flyrnai.org/evaluateCrispr/ DRSC, Harvard Medical School, Boston, MA, USA]
 +
* <b>DRSC Finding CRISPRs</b>, Drosophila CRISPR gRNA design search tool:<br />[http://www.flyrnai.org/crispr2/ DRSC, Harvard Medical School, Boston, MA, USA]
 
* <b>E-CRISP</b>, Design of CRISPR Constructs:<br />[http://www.e-crisp.org/E-CRISP/designcrispr.html DKFZ/Boutros lab, Heildelberg, Germany]
 
* <b>E-CRISP</b>, Design of CRISPR Constructs:<br />[http://www.e-crisp.org/E-CRISP/designcrispr.html DKFZ/Boutros lab, Heildelberg, Germany]
 
* <b>E-TALEN</b>, Design of TALEN Constructs:<br />[http://www.e-talen.org/E-TALEN/ DKFZ/Boutros lab, Heildelberg, Germany]
 
* <b>E-TALEN</b>, Design of TALEN Constructs:<br />[http://www.e-talen.org/E-TALEN/ DKFZ/Boutros lab, Heildelberg, Germany]
* <b>Finding CRISPRs</b>, Drosophila CRISPR gRNA design search tool:<br />[http://www.flyrnai.org/crispr2/ DRSC, Harvard Medical School, Boston, MA, USA]
 
 
* <b>flyCRISPR</b>, Resource Site: <br />[http://flycrispr.molbio.wisc.edu/ O'Connor-Giles, Wildonger, and Harrison Labs, University of Wisconsin-Madison, WI, USA]
 
* <b>flyCRISPR</b>, Resource Site: <br />[http://flycrispr.molbio.wisc.edu/ O'Connor-Giles, Wildonger, and Harrison Labs, University of Wisconsin-Madison, WI, USA]
 
* <b>flyCRISPR</b>, Optimal Target Finder:<br />[http://tools.flycrispr.molbio.wisc.edu/targetFinder/ O'Connor-Giles Lab, University of Wisconsin-Madison, WI, USA]
 
* <b>flyCRISPR</b>, Optimal Target Finder:<br />[http://tools.flycrispr.molbio.wisc.edu/targetFinder/ O'Connor-Giles Lab, University of Wisconsin-Madison, WI, USA]
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* <b>BDGP in situ</b>, Patterns of gene expression in Drosophila embryogenesis:<br />[http://insitu.fruitfly.org/cgi-bin/ex/insitu.pl Gene expression database, BDGP, University of California, Berkeley, USA]
 
* <b>BDGP in situ</b>, Patterns of gene expression in Drosophila embryogenesis:<br />[http://insitu.fruitfly.org/cgi-bin/ex/insitu.pl Gene expression database, BDGP, University of California, Berkeley, USA]
 
* <b>BDTNP</b>, A cellular resolution 3D gene expression and morphology Atlas of the blastoderm.<br />[http://bdtnp.lbl.gov/Fly-Net/bioimaging.jsp?w=summary Berkeley Drosophila Transcription Network Project, University of California, Berkeley, USA]
 
* <b>BDTNP</b>, A cellular resolution 3D gene expression and morphology Atlas of the blastoderm.<br />[http://bdtnp.lbl.gov/Fly-Net/bioimaging.jsp?w=summary Berkeley Drosophila Transcription Network Project, University of California, Berkeley, USA]
 +
* <b>BGee</b> Normal Gene Expression Data in Animals (based on RNA-Seq, Affymetrix, in situ hybridization, and EST data).<br />[http://bgee.org/ SIB, Swiss Institute of Bioinformatics, University of Lausanne, Lausanne, Switzerland]
 
* <b><em>cis</em>Patterns</b>, A database of over 100 Drosophila GAL4-driver lines regulated by single cis-regulatory enhancers:<br />[http://cispatterns.ninds.nih.gov/ Jermaine Ross and the Odenwald Lab, NINDS, NIH, Bethesda MD, USA]
 
* <b><em>cis</em>Patterns</b>, A database of over 100 Drosophila GAL4-driver lines regulated by single cis-regulatory enhancers:<br />[http://cispatterns.ninds.nih.gov/ Jermaine Ross and the Odenwald Lab, NINDS, NIH, Bethesda MD, USA]
 
* <b>DGRC, Cell Line Expression tool</b> (based on modENCODE data):<br />[https://dgrc.cgb.indiana.edu/cells/TilingSearch DGRC, University of Indiana, Bloomington, IN, USA]
 
* <b>DGRC, Cell Line Expression tool</b> (based on modENCODE data):<br />[https://dgrc.cgb.indiana.edu/cells/TilingSearch DGRC, University of Indiana, Bloomington, IN, USA]
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* <b>FlyGut-seq</b>, a transcriptomic resource that complements the original [http://flygut.epfl.ch/ Flygut website]:<br />[http://flygutseq.buchonlab.com/ Buchon Lab, Cornell University, Ithaca, NY, USA]
 
* <b>FlyGut-seq</b>, a transcriptomic resource that complements the original [http://flygut.epfl.ch/ Flygut website]:<br />[http://flygutseq.buchonlab.com/ Buchon Lab, Cornell University, Ithaca, NY, USA]
 
* <b>FlyLight</b>, Expression Patterns of GAL4 Driver Lines:<br />[http://flweb.janelia.org/cgi-bin/flew.cgi HHMI, Janelia Farms Research Campus]
 
* <b>FlyLight</b>, Expression Patterns of GAL4 Driver Lines:<br />[http://flweb.janelia.org/cgi-bin/flew.cgi HHMI, Janelia Farms Research Campus]
 +
* <b>FlyOde</b>, FLY Organ Developmental Network: <br /> [http://flyode.boun.edu.tr/index.html FlyOde, Bogazici University, Istanbul, Turkey]
 
* <b>flytrap</b>, a database of P{GAL4} enhancer traps and their expression in brains: <br />[http://www.fly-trap.org/ flytrap, University of Edinburgh, UK]
 
* <b>flytrap</b>, a database of P{GAL4} enhancer traps and their expression in brains: <br />[http://www.fly-trap.org/ flytrap, University of Edinburgh, UK]
 
* <b>GEO Profiles</b>, Gene Expression Omnibus:<br />[http://www.ncbi.nlm.nih.gov/geo/info/profiles.html GEO, NCBI, Bethesda, MD USA]
 
* <b>GEO Profiles</b>, Gene Expression Omnibus:<br />[http://www.ncbi.nlm.nih.gov/geo/info/profiles.html GEO, NCBI, Bethesda, MD USA]
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=Gene Groups=
 
=Gene Groups=
* <b>FlyBase Gene Group Reports</b>:<br />[http://flybase.org/static_pages/feature/previous/articles/2015_05/gene_groups.html FlyBase Consortium]
+
* <b>FlyBase Gene Groups</b>, Reports on functionally related genes:<br /> [http://flybase.org/static_pages/FBgg/browse.html Gene group list, FlyBase, Bloomington, IN and Cambridge, MA, USA, Cambridge, UK]
 
* <b>GLAD</b>, an Online Database of Gene List Annotations for Drosophila:<br /> [http://www.flyrnai.org/tools/glad/web/ DRSC, Harvard Medical School, Boston, MA, USA]
 
* <b>GLAD</b>, an Online Database of Gene List Annotations for Drosophila:<br /> [http://www.flyrnai.org/tools/glad/web/ DRSC, Harvard Medical School, Boston, MA, USA]
 +
* <b>Interactive fly</b>, Drosophila genes listed by biochemical function:<br /> [http://www.sdbonline.org/sites/fly/aimain/6biochem.htm Interactive Fly, Thomas Brody and Society for Developmental Biology, MD, USA]
 +
* <b>Interactive fly</b>, Maternally transcribed genes:<br /> [http://www.sdbonline.org/sites/fly/aimain/4matrnl.htm Interactive Fly, Thomas Brody and Society for Developmental Biology, MD, USA]
 +
* <b>Interactive fly</b>, Zygotically transcribed genes:<br /> [http://www.sdbonline.org/sites/fly/aimain/5zygotic.htm Interactive Fly, Thomas Brody and Society for Developmental Biology, MD, USA]
 +
* <b>KEGG BRITE</b>, Functional hierarchies and binary relationships of biological entities:<br /> [http://www.genome.jp/kegg/brite.html KEGG, Kyoto University, Kyoto, Japan and University of Tokyo, Tokyo, Japan]
 +
* <b>UCSC D. melanogaster Gene Sorter</b>, displays tables of genes related by a variety of characteristics including protein-level homology, similarity of gene expression profiles, and genomic proximity.:<br /> [https://genome.ucsc.edu/cgi-bin/hgNear?org=D.+melanogaster UCSC Genome Informatics Group, University of California, Santa Cruz, Santa Cruz, CA, USA]
  
 
=General Bioinformatics Tools=
 
=General Bioinformatics Tools=
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* <b>BioMart</b>, Data Warehouse:<br />[http://www.biomart.org/ BioMart, EMBL-EBI, OICR, SRSI]
 
* <b>BioMart</b>, Data Warehouse:<br />[http://www.biomart.org/ BioMart, EMBL-EBI, OICR, SRSI]
 
* <b>Cytoscape</b> -- Network Data Integration, Analysis, and Visualization in a Box:<br />[http://www.cytoscape.org/ Cytoscape, Cytoscape Consortium, Canada, France, and USA]
 
* <b>Cytoscape</b> -- Network Data Integration, Analysis, and Visualization in a Box:<br />[http://www.cytoscape.org/ Cytoscape, Cytoscape Consortium, Canada, France, and USA]
* <b>DAVID (NIH)</b> -- Database for Annotation , Visualization and Integrated Discovery:<br />[http://david.abcc.ncifcrf.gov/ DAVID, NIH, Bethesda, MD, USA]
 
 
* <b>DNA & Protein Work List</b>, A list of tools aggregated by the Prokop Lab:<br />[http://www.prokop.co.uk/Links/tools.html http://www.prokop.co.uk/Links/tools.html]
 
* <b>DNA & Protein Work List</b>, A list of tools aggregated by the Prokop Lab:<br />[http://www.prokop.co.uk/Links/tools.html http://www.prokop.co.uk/Links/tools.html]
 
* <b>FlyMine</b>, an Integrated Database for Drosophila and Anopheles Genomics:<br />[http://www.flymine.org/ University of Cambridge, United Kingdom]
 
* <b>FlyMine</b>, an Integrated Database for Drosophila and Anopheles Genomics:<br />[http://www.flymine.org/ University of Cambridge, United Kingdom]
Line 112: Line 123:
 
* <b>Galaxy</b>: Open Source Bioinformatics Tools:<br />[https://usegalaxy.org/ Galaxy, Penn State, PA USA and Emory University, GA USA]
 
* <b>Galaxy</b>: Open Source Bioinformatics Tools:<br />[https://usegalaxy.org/ Galaxy, Penn State, PA USA and Emory University, GA USA]
 
* <b>GSEA</b>, Gene Set Enrichment Analysis:<br />[http://www.broadinstitute.org/gsea/index.jsp GSEA, Broad Institute, Cambridge, MA, USA]
 
* <b>GSEA</b>, Gene Set Enrichment Analysis:<br />[http://www.broadinstitute.org/gsea/index.jsp GSEA, Broad Institute, Cambridge, MA, USA]
* <b>GOrilla</b> -- Gene Ontology enRIchment and anaLysis and viuaLizAtion tool:<br />[http://cbl-gorilla.cs.technion.ac.il/ GOrilla, Israel]
 
  
 
=Genome Sequencing Projects=
 
=Genome Sequencing Projects=
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* <b>FlyNet Human Disease Prioritization</b>:<br /> [http://www.inetbio.org/flynet/Network_fly_comm.php NetBioLab, Yonsei University, Seoul, Korea]
 
* <b>FlyNet Human Disease Prioritization</b>:<br /> [http://www.inetbio.org/flynet/Network_fly_comm.php NetBioLab, Yonsei University, Seoul, Korea]
 
* <b>HuDis</b>, high confidence human disease gene - fly gene ortholog pairs:<br />[http://www.flyrnai.org/HuDis DRSC, Harvard Medical School, Boston, MA, USA]
 
* <b>HuDis</b>, high confidence human disease gene - fly gene ortholog pairs:<br />[http://www.flyrnai.org/HuDis DRSC, Harvard Medical School, Boston, MA, USA]
 +
* <b>MORPHIN</b>, Model ORganism Projected on a Human Integrated gene Network:<br />[http://www.inetbio.org/morphin/index.php MORPHIN, Lee Lab, Yonsei University, Korea and Marcotte Lab, University of Texas at Austin, USA.]
 +
* <b>NeuroGeM</b>, A knowledgebase of genetic modifiers in neurodegenerative diseases:<br />[http://chibi.ubc.ca/neurogem/ CHiBi, The University of British Columbia, Vancouver, BC, Canada]
  
 
=Interaction and Pathway Databases=
 
=Interaction and Pathway Databases=
 
* <b>BioGRID</b>, The General Repository for Interaction Datasets:<br />[http://www.thebiogrid.org/index.php BioGRID, Mount Sinai Hospital, Toronto, Canada]
 
* <b>BioGRID</b>, The General Repository for Interaction Datasets:<br />[http://www.thebiogrid.org/index.php BioGRID, Mount Sinai Hospital, Toronto, Canada]
 
* <b>COMPLEAT</b>, protein COMPLex Enrichment Analysis Tool:<br />[http://www.flyrnai.org/compleat/ COMPLEAT, DRSC, Harvard Medical School, Boston, MA, USA]
 
* <b>COMPLEAT</b>, protein COMPLex Enrichment Analysis Tool:<br />[http://www.flyrnai.org/compleat/ COMPLEAT, DRSC, Harvard Medical School, Boston, MA, USA]
 +
* <b>DAPPER</b>, database for protein-protein interactions:<br/>[http://dapper.gen.cam.ac.uk/ DAPPER, University of Cambridge, Cambridge, UK]
 
* <b>DPiM</b>, Drosophila Protein interaction Map:<br />[https://interfly.med.harvard.edu/ DPiM, Harvard University Medical School, Boston, MA, USA]
 
* <b>DPiM</b>, Drosophila Protein interaction Map:<br />[https://interfly.med.harvard.edu/ DPiM, Harvard University Medical School, Boston, MA, USA]
 
* <b>DroID</b>, Drosophila Interactions Database:<br />[http://www.droidb.org/ Drosophila Interaction Database, Detroit, USA]
 
* <b>DroID</b>, Drosophila Interactions Database:<br />[http://www.droidb.org/ Drosophila Interaction Database, Detroit, USA]
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* <b>FlyCyc</b> -- Curated Drosophila melanogaster Pathways:<br />[http://biocyc.org/FLY/organism-summary?object=FLY FlyCyc, Harvard University, Cambridge, USA]
 
* <b>FlyCyc</b> -- Curated Drosophila melanogaster Pathways:<br />[http://biocyc.org/FLY/organism-summary?object=FLY FlyCyc, Harvard University, Cambridge, USA]
 
* <b>FlyNet Gene Prioritization</b>: <br /> [http://www.inetbio.org/flynet/Network_gene_prioritization.php NetBioLab, Yonsei University, Seoul, Korea]
 
* <b>FlyNet Gene Prioritization</b>: <br /> [http://www.inetbio.org/flynet/Network_gene_prioritization.php NetBioLab, Yonsei University, Seoul, Korea]
 +
* <b>FlyOde</b>, FLY Organ Developmental Network: <br /> [http://flyode.boun.edu.tr/index.html FlyOde, Bogazici University, Istanbul, Turkey]
 
* <b>FlyReactome</b> -- a Curated Knowledgebase of Drosophila melanogaster Pathways:<br />[http://fly.reactome.org FlyReactome, University of Cambridge, Cambridge, UK]
 
* <b>FlyReactome</b> -- a Curated Knowledgebase of Drosophila melanogaster Pathways:<br />[http://fly.reactome.org FlyReactome, University of Cambridge, Cambridge, UK]
 
* <b>IM Browser</b>, Drosophila Interactions Database:<br />[http://proteome.wayne.edu/PIMdb.html IM Browser, Wayne State University, Detroit, MI, USA]
 
* <b>IM Browser</b>, Drosophila Interactions Database:<br />[http://proteome.wayne.edu/PIMdb.html IM Browser, Wayne State University, Detroit, MI, USA]
Line 141: Line 155:
 
* <b>KEGG</b> -- Kyoto Encyclopedia of Genes and Genomes:<br />[http://www.genome.jp/kegg KEGG, Kyoto, Japan]
 
* <b>KEGG</b> -- Kyoto Encyclopedia of Genes and Genomes:<br />[http://www.genome.jp/kegg KEGG, Kyoto, Japan]
 
* <b>Reactome Pathway Database</b>:<br />[http://www.reactome.org/ Reactome, OICR, Ontario, Canada, EMBL-EBI, UK, NYU Medical Center, NY, USA]
 
* <b>Reactome Pathway Database</b>:<br />[http://www.reactome.org/ Reactome, OICR, Ontario, Canada, EMBL-EBI, UK, NYU Medical Center, NY, USA]
 +
* <b>SignaLink</b>, A signaling pathway resource with multi-layered regulatory networks:<br />[http://http://signalink.org/ SignaLink, Eötvös Loránd University of Science, Budapest, Hungary]
 
* <b>SignedPPI</b>, Searchable Database of Known and Predicted Protein-protein Interactions:<br />[http://www.flyrnai.org/SignedPPI/ DRSC, Harvard Medical School, Boston, MA, USA]
 
* <b>SignedPPI</b>, Searchable Database of Known and Predicted Protein-protein Interactions:<br />[http://www.flyrnai.org/SignedPPI/ DRSC, Harvard Medical School, Boston, MA, USA]
 
* <b>STRING</b>, Known and Predicted Protein-Protein Interactions<br />[http://string-db.org/ STRING, SIB, Switzerland CPR, Denmark, and EMBL, Heidelberg, Germany]
 
* <b>STRING</b>, Known and Predicted Protein-Protein Interactions<br />[http://string-db.org/ STRING, SIB, Switzerland CPR, Denmark, and EMBL, Heidelberg, Germany]
 +
* <b>WikiPathways</b>, an open, public platform dedicated to the curation of biological pathways by and for the scientific community:<br />[http://www.wikipathways.org/index.php/WikiPathways WikiPathways, Gladstone Institute, San Francisco, CA, USA and Maastricht University, The Netherlands]
  
 
=Laboratory Resources=
 
=Laboratory Resources=
 
* <b>Laboratory Manual of Drosophila</b>: <br />[http://darwin.bio.uci.edu/~mueller/pdf/Lab_manual.pdf PDF, Chippindale, A. ''et al''., Department of Ecology & Evolutionary Biology, University of California, Irvine, USA]
 
* <b>Laboratory Manual of Drosophila</b>: <br />[http://darwin.bio.uci.edu/~mueller/pdf/Lab_manual.pdf PDF, Chippindale, A. ''et al''., Department of Ecology & Evolutionary Biology, University of California, Irvine, USA]
 
=miRNA and ncRNA Databases and Tools=
 
* <b>DIANA microT-CDS</b>, MicroRNA Target Prediction:<br />[http://diana.imis.athena-innovation.gr/DianaTools/ DIANA microT-CDS, DIANA LAB, Athens, Greece]
 
* <b>DIANA TarBase</b>, MicroRNA Target Database:<br />[http://diana.imis.athena-innovation.gr/DianaTools/ DIANA TarBase,, DIANA LAB, Athens, Greece]
 
* <b>MinoTar</b>, Predict microRNA Targets in Coding Sequence:<br />[http://www.flyrnai.org/cgi-bin/DRSC_MinoTar.pl MinoTar, DRSC, Harvard Medical School, Boston, MA, USA]
 
* <b>miRBase</b>, microRNA data:<br />[http://www.mirbase.org/ 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.
 
* <b>miRNA, Target Gene Prediction</b>:<br />[http://www.mirna.embl.de/ miRNA - Target Prediction, EMBL, Heidelberg, Germany]
 
* <b>miRNA_Targets</b>:<br />[http://mamsap.it.deakin.edu.au/~amitkuma/mirna_targetsnew/index.html miRNA targets on full length mRNAs, Deakin University, Victoria, Australia]
 
* <b>miRTarBase</b>, Experimentally Validated microRNA-target Interactions Database:<br />[http://mirtarbase.mbc.nctu.edu.tw/ miRTarBase, ISBLab, Hsinchu, Taiwan]
 
* <b>Rfam</b>, RNA families database of alignments and CMs:<br />[http://www.webcitation.org/getfile?fileid=db1c351a4c279e9cf9697bd2d1962097900701fb Rfam, Wellcome Trust Sanger Institute, Hinxton, UK and Janelia Farm, Ashburn, VA, USA]
 
* <b>TargetScanFly</b>, Prediction of microRNA targets:<br />[http://www.targetscan.org/fly_12/ TargetScanFly, Whitehead Institute and MIT Dept. of Biology, USA]]
 
  
 
=Miscellaneous=
 
=Miscellaneous=
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* <b>GenAge</b> -- The Ageing Gene Database:<br />[http://genomics.senescence.info/genes/ Human Ageing Genomic Resources, Institute of Integrative Biology, Liverpool, UK]
 
* <b>GenAge</b> -- The Ageing Gene Database:<br />[http://genomics.senescence.info/genes/ Human Ageing Genomic Resources, Institute of Integrative Biology, Liverpool, UK]
 
* <b>Gene Lookup</b>, Gene and Reagent Lookup:<br />[http://www.flyrnai.org/cgi-bin/DRSC_gene_lookup.pl Gene Lookup, DRSC, Harvard Medical School, Boston, MA, USA]
 
* <b>Gene Lookup</b>, Gene and Reagent Lookup:<br />[http://www.flyrnai.org/cgi-bin/DRSC_gene_lookup.pl Gene Lookup, DRSC, Harvard Medical School, Boston, MA, USA]
 +
* <b>IGTRCN</b>, Insect Genetic Technologies Research Coordination Network:<br />[http://igtrcn.org// IGTRCN, University of Maryland, Rockville, MD, USA]
 
* <b>Interactive Fly</b>, A cyberspace guide to Drosophila development and metazoan evolution<br />[http://www.sdbonline.org/fly/aimain/1aahome.htm Interactive Fly, Bethesda, MD, USA]
 
* <b>Interactive Fly</b>, A cyberspace guide to Drosophila development and metazoan evolution<br />[http://www.sdbonline.org/fly/aimain/1aahome.htm Interactive Fly, Bethesda, MD, USA]
 
* <b>Jfly</b>, a data depository for the fly and other insects, with an emphasis for the Japanese-speaking fly community:<br />[http://jfly.iam.u-tokyo.ac.jp/ Jfly, University of Tokyo, Japan]
 
* <b>Jfly</b>, a data depository for the fly and other insects, with an emphasis for the Japanese-speaking fly community:<br />[http://jfly.iam.u-tokyo.ac.jp/ Jfly, University of Tokyo, Japan]
Line 178: Line 183:
 
* <b>What's hot today:</b> Current papers in developmental biology and gene function:<br />[http://www.sdbonline.org/sites/fly/aimain/model-organisms-this-week.htm Interactive Fly, Bethesda, MD, USA]
 
* <b>What's hot today:</b> Current papers in developmental biology and gene function:<br />[http://www.sdbonline.org/sites/fly/aimain/model-organisms-this-week.htm Interactive Fly, Bethesda, MD, USA]
 
* <b>The WWW Virtual Library--Drosophila</b>:<br />[http://www.ceolas.org/fly/ Drosophila Virtual Library]
 
* <b>The WWW Virtual Library--Drosophila</b>:<br />[http://www.ceolas.org/fly/ Drosophila Virtual Library]
 +
 +
=ncRNA Databases and Tools=
 +
* <b>DIANA microT-CDS</b>, MicroRNA Target Prediction:<br />[http://diana.imis.athena-innovation.gr/DianaTools/index.php?r=microT_CDS/index DIANA microT-CDS, DIANA LAB, Athens, Greece]
 +
* <b>DIANA TarBase</b>, MicroRNA Target Database:<br />[http://diana.imis.athena-innovation.gr/DianaTools/index.php?r=tarbase/index DIANA TarBase, DIANA LAB, Athens, Greece]
 +
* <b>GtRNAdb</b>, tRNAscan-SE analysis of complete genomes:<br />[http://gtrnadb.ucsc.edu/ GtRNAdb, Lowe lab, University of California, Santa Cruz, Santa Cruz, CA, USA]
 +
* <b>MinoTar</b>, Predict microRNA Targets in Coding Sequence:<br />[http://www.flyrnai.org/cgi-bin/DRSC_MinoTar.pl MinoTar, DRSC, Harvard Medical School, Boston, MA, USA]
 +
* <b>miRBase</b>, microRNA data:<br />[http://www.mirbase.org/ 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.
 +
* <b>miRNA, Target Gene Prediction</b>:<br />[http://www.mirna.embl.de/ miRNA - Target Prediction, EMBL, Heidelberg, Germany]
 +
* <b>miRNA_Targets</b>:<br />[http://mamsap.it.deakin.edu.au/~amitkuma/mirna_targetsnew/index.html miRNA targets on full length mRNAs, Deakin University, Victoria, Australia]
 +
* <b>miRTarBase</b>, Experimentally Validated microRNA-target Interactions Database:<br />[http://mirtarbase.mbc.nctu.edu.tw/ miRTarBase, ISBLab, Hsinchu, Taiwan]
 +
* <b>Rfam</b>, RNA families database of alignments and CMs:<br />[http://www.webcitation.org/getfile?fileid=db1c351a4c279e9cf9697bd2d1962097900701fb Rfam, Wellcome Trust Sanger Institute, Hinxton, UK and Janelia Farm, Ashburn, VA, USA]
 +
* <b>RNAcentral</b>, provides unified access to the ncRNA sequence data supplied by multiple Expert Databases:<br />[http://rnacentral.org/ RNAcentral, EMBL-EBI, Hingston, UK]
 +
* <b>snOPY</b>, a snoRNA orthological gene database providing comprehensive information about snoRNAs, snoRNA gene loci and target RNAs.:<br />[http://snoopy.med.miyazaki-u.ac.jp/ snOPY, University of Miyazaki, Japan ]
 +
* <b>TargetScanFly</b>, Prediction of microRNA targets:<br />[http://www.targetscan.org/fly_12/ TargetScanFly, Whitehead Institute and MIT Dept. of Biology, USA]]
 +
 +
=Ontology Resources=
 +
* <b>AmiGO 2</b>, tools for searching and browsing the Gene Ontology database:<br />[http://amigo2.berkeleybop.org/amigo AmiGO 2, Berkeley Bioinformatics Open-source Projects, USA]
 +
* <b>BioPortal</b>, a biomedical ontologies repository and browser:<br />[http://bioportal.bioontology.org/ BioPortal, The National Center for Biomedical Ontology, USA]
 +
* <b>Disease Ontology</b>, ontology of disease terms:<br />[http://disease-ontology.org/ Disease Ontology]
 +
* <b>Gene Ontology Consortium</b><br />[http://geneontology.org/ Gene Ontology Consortium]
 +
* <b>GOrilla</b> -- Gene Ontology enRIchment and anaLysis and viuaLizAtion tool:<br />[http://cbl-gorilla.cs.technion.ac.il/ GOrilla, Israel]
 +
* <b>OboEdit</b>, browser for OBO ontologies:<br />[http://oboedit.org/ OboEdit]
 +
* <b>The OBO Foundry</b>, an ontology registry:<br />[http://obofoundry.github.io/ OboFoundry]
 +
* <b>Ontobee</b>, an ontologies browser:<br />[http://www.ontobee.org/ Ontobee, He Group, University of Michigan Medical School, Ann Arbor, Michigan, USA]
 +
* <b>Ontology Lookup Service</b>, an ontologies browser:<br />[http://www.ebi.ac.uk/ontology-lookup/ Ontology Lookup Service, EMBL-EBI, Hinxton, UK]
 +
* <b>Protege</b>, browser for OWL ontologies:<br />[http://protege.stanford.edu/products.php, Protege, Stanford Center for Biomedical Informatics Research, Stanford University School of Medicine, USA]
 +
* <b>QuickGO</b>, a browser for Gene Ontology terms and annotations:<br />[http://www.ebi.ac.uk/QuickGO/ QuickGO, EMBL-EBI, Hinxton, UK]
 +
 +
=Orthology Predictions=
 +
* <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>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 DRSC, Harvard Medical School, Boston, MA, USA]
 +
* <b>EggNOG</b>, A database of orthologous groups and functional annotation:<br />[http://eggnogdb.embl.de/#/app/home Computational Biology Group, EMBL, Heidelberg, Germany]
 +
* <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>OrthoDB</b>, The Hierarchical Catalog of Orthologs<br />[http://orthodb.org/ Zdobnov Computational Evolutionary Genomics group, University of Geneva, Geneva, Switzerland]
 +
* <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=
Line 183: Line 231:
 
* <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</b>, DRSC Integrative Ortholog Prediction Tool:<br />[http://www.flyrnai.org/cgi-bin/DRSC_orthologs.pl DRSC, Harvard Medical School, Boston, MA, USA]
 
* <b>EvoPrinter</b>, Identification of Evolutionarily Resilient DNA Sequences<br />[http://evoprinter.ninds.nih.gov/ NINDS, NIH, Bethesda MD, USA]
 
* <b>EvoPrinter</b>, Identification of Evolutionarily Resilient DNA Sequences<br />[http://evoprinter.ninds.nih.gov/ NINDS, NIH, Bethesda MD, USA]
 +
* <b>HomoloGene</b> -- automated system fo constructing putative homology groups:<br />[http://www.ncbi.nlm.nih.gov/homologene NCBI, Bethesda, MA, USA]
 
* <b>InParanoid</b>, Eukaryotic Ortholog Groups:<br />[http://inparanoid.sbc.su.se/cgi-bin/index.cgi InParanoid, Karolinska Institute, Sweden]
 
* <b>InParanoid</b>, Eukaryotic Ortholog Groups:<br />[http://inparanoid.sbc.su.se/cgi-bin/index.cgi InParanoid, Karolinska Institute, Sweden]
 
* <b>MANTiS</b>, a phylogenetic framework for multi-species genome comparisons:<br />[http://www.mantisdb.org/MANTiS/Welcome.html MANTiS, Université Libre de Bruxelles, Belgium]
 
* <b>MANTiS</b>, a phylogenetic framework for multi-species genome comparisons:<br />[http://www.mantisdb.org/MANTiS/Welcome.html MANTiS, Université Libre de Bruxelles, Belgium]
* <b>NCBI HomoloGene</b> -- automated system fo constructing putative homology groups:<br />[http://www.ncbi.nlm.nih.gov/homologene NCBI, Bethesda, MA, USA]
 
 
* <b>OrthoDB</b>, the Hierarchical Catalog of Orthologs:<br />http://orthodb.org/orthodb7 OrthoDB, University of Geneva, Switzerland]
 
* <b>OrthoDB</b>, the Hierarchical Catalog of Orthologs:<br />http://orthodb.org/orthodb7 OrthoDB, University of Geneva, Switzerland]
 
* <b>Vista Tools</b> -- Whole Genome Comparative Analysis of the D. melanogaster (CAF1) Genome:<br />[http://pipeline.lbl.gov/cgi-bin/gateway2?bg=droMel_caf1&selector=vistapoint Whole Genome Comparative Analysis of the D. melanogaster (CAF1) Genome, LBNL, USA]
 
* <b>Vista Tools</b> -- Whole Genome Comparative Analysis of the D. melanogaster (CAF1) Genome:<br />[http://pipeline.lbl.gov/cgi-bin/gateway2?bg=droMel_caf1&selector=vistapoint Whole Genome Comparative Analysis of the D. melanogaster (CAF1) Genome, LBNL, USA]
Line 202: Line 250:
 
* <b>ExPASy</b>, the SIB Bioinformatics Resource Portal which provides access to scientific databases and software tools in different areas of life sciences:<br />[http://expasy.org/ SIB Swiss Institute of Bioinformatics, Genève, Switzerland]
 
* <b>ExPASy</b>, the SIB Bioinformatics Resource Portal which provides access to scientific databases and software tools in different areas of life sciences:<br />[http://expasy.org/ SIB Swiss Institute of Bioinformatics, Genève, Switzerland]
 
* <b>GPCRDB</b>, information system for G protein-coupled receptors (GPCRs):<br />[http://www.gpcr.org/7tm/ GPCRDB, The GPCRDB (G Protein-Coupled Receptor Data Base) partnership]
 
* <b>GPCRDB</b>, information system for G protein-coupled receptors (GPCRs):<br />[http://www.gpcr.org/7tm/ GPCRDB, The GPCRDB (G Protein-Coupled Receptor Data Base) partnership]
* <b>InterPro protein domain analysis of Drosophila</b>:<br />[http://www.ebi.ac.uk/interpro/ InterPro: protein sequence analysis & classification, EBI, UK]
+
* <b>InterPro</b> protein domain analysis of Drosophila:<br />[http://www.ebi.ac.uk/interpro/ InterPro: protein sequence analysis & classification, EBI, UK]
 
* <b>MEROPS</b>, an information resource for peptidases:<br />[http://merops.sanger.ac.uk/ MEROPS, Wellcome Trust Sanger Institute, Hinxton, UK]
 
* <b>MEROPS</b>, an information resource for peptidases:<br />[http://merops.sanger.ac.uk/ MEROPS, Wellcome Trust Sanger Institute, Hinxton, UK]
* <b>Panther protein classification system</b>:<br />[http://panther.appliedbiosystems.com/about.jsp Panther Protein Classification System, Applied Biosystems &amp; Celera, USA]
+
* <b>Panther (Protein Analysis THrough Evolutionary Relationships)</b> protein classification system:<br />[http://panther.appliedbiosystems.com/about.jsp Panther Protein Classification System, Applied Biosystems &amp; Celera, USA]
 
* <b>PDB</b>, Protein Data Bank:<br />[http://www.rcsb.org/pdb/home/home.do PDB, The Research Collaboratory for Structural Bioinformatics (RCSB) consortium]
 
* <b>PDB</b>, Protein Data Bank:<br />[http://www.rcsb.org/pdb/home/home.do PDB, The Research Collaboratory for Structural Bioinformatics (RCSB) consortium]
 
* <b>PhospoPep</b>, interactive interrogation of MS-derived phosphorylation data from 4 different organisms: <br />[http://www.phosphopep.org/index.php Institute for Systems Biology, Seattle, Washington, USA]
 
* <b>PhospoPep</b>, interactive interrogation of MS-derived phosphorylation data from 4 different organisms: <br />[http://www.phosphopep.org/index.php Institute for Systems Biology, Seattle, Washington, USA]
Line 265: Line 313:
 
* <b>EPD</b>, the Eukaryotic Promoter Database:<br />[http://www.epd.isb-sib.ch/ EPD, Epalinges s/Lausanne, Switzerland]
 
* <b>EPD</b>, the Eukaryotic Promoter Database:<br />[http://www.epd.isb-sib.ch/ EPD, Epalinges s/Lausanne, Switzerland]
 
* <b>Fly Factor Survey</b> - Database of Drosophila TF DNA-binding Specificitiies: <br />[http://pgfe.umassmed.edu/ffs/ FLy Factor Survey, UMass Medical School, Worcester, MA, USA]
 
* <b>Fly Factor Survey</b> - Database of Drosophila TF DNA-binding Specificitiies: <br />[http://pgfe.umassmed.edu/ffs/ FLy Factor Survey, UMass Medical School, Worcester, MA, USA]
 +
* <b>i-cisTarget</b>, An integrative genomics method for the prediction of regulatory features and cis-regulatory modules in Human, Mouse, and Fly:<br />[http://gbiomed.kuleuven.be/apps/lcb/i-cisTarget/ i-cisTarget, University of Leuven, Leuven, Belgium]
 +
* <b>Neural Network Promoter Prediction for Drosophila</b>:<br />[http://www.fruitfly.org/seq_tools/promoter.html Neural Network Promoter Prediction, Berkeley Drosophila Genome Project, University of California, Berkeley, USA]
 
* <b>OnTheFly</b>, Database of Drosophila Transcription Factors and Transcription Factor Binding Sites <br />[https://bhapp.c2b2.columbia.edu/OnTheFly/index.php OnTheFly, Columbia University, USA]
 
* <b>OnTheFly</b>, Database of Drosophila Transcription Factors and Transcription Factor Binding Sites <br />[https://bhapp.c2b2.columbia.edu/OnTheFly/index.php OnTheFly, Columbia University, USA]
* <b>Neural Network Promoter Prediction for Drosophila</b>:<br />[http://www.fruitfly.org/seq_tools/promoter.html Neural Network Promoter Prediction, Berkeley Drosophila Genome Project, University of California, Berkeley, USA]
 
 
* <b>PREdictor</b>, to identify Polycomb/Trithorax response elements: <br />[http://bibiserv.techfak.uni-bielefeld.de/predictor/ PREdictor, Bielefeld University, Germany]
 
* <b>PREdictor</b>, to identify Polycomb/Trithorax response elements: <br />[http://bibiserv.techfak.uni-bielefeld.de/predictor/ PREdictor, Bielefeld University, Germany]
 
* <b>REDfly</b>, Regulatory Element Database for Drosophila:<br />[http://redfly.ccr.buffalo.edu/ REDfly, University at Buffalo, New York, USA]
 
* <b>REDfly</b>, Regulatory Element Database for Drosophila:<br />[http://redfly.ccr.buffalo.edu/ REDfly, University at Buffalo, New York, USA]

Revision as of 16:15, 3 October 2015

Atlases, Images and Videos

CRISPRs and TALENs

Data Repositories

Data and Metadata for Drosophila Genomes

Gene Expression Databases and Tools

Gene Groups

General Bioinformatics Tools

Genome Sequencing Projects

Human Disease: Drosophila Models and Orthologous Genes

Interaction and Pathway Databases

Laboratory Resources

Miscellaneous

ncRNA Databases and Tools

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.

Ontology Resources

Orthology Predictions

Phylogenetic Comparison Tools

Population Biology and Polymorphism Resources

Protein Analysis

Public Education

RNAi

Sequence Analysis

Taxonomy

Transcription Regulation Databases and Tools

Suggest a tool or resource