Difference between revisions of "FlyBase:Drosophila Online Resources"
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=Atlases, Images and Videos= | =Atlases, Images and Videos= | ||
| − | * BDTNP, 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] |
| − | * CSIRO Anatomical Atlas of Flies:<br />[http://www.ento.csiro.au/biology/fly/fly.html# CSIRO Entomology, Australia] | + | * <b>CSIRO</b> Anatomical Atlas of Flies:<br />[http://www.ento.csiro.au/biology/fly/fly.html# CSIRO Entomology, Australia] |
| − | * Electron micrograph maps of ''D. melanogaster'' polytene chromosomes:<br />[http://www.helsinki.fi/~saura/EM/index.html Sorsa Maps, Helsinki, Finland] | + | * <b>Electron micrograph maps</b> of ''D. melanogaster'' polytene chromosomes:<br />[http://www.helsinki.fi/~saura/EM/index.html Sorsa Maps, Helsinki, Finland] |
| − | * FlyBrain, an Online Atlas and Database of the Drosophila Nervous System:<br />[http://flybrain.neurobio.arizona.edu/ FlyBrain, University of Arizona, Tucson, USA] | + | * <b>FlyBrain</b>, an Online Atlas and Database of the Drosophila Nervous System:<br />[http://flybrain.neurobio.arizona.edu/ FlyBrain, University of Arizona, Tucson, USA] |
| − | * FlyCircuit, a Database of Drosophila Brain Neurons:<br />[http://www.flycircuit.tw/ FlyCircuit, National Tsing Hua University, Taiwan] | + | * <b>FlyCircuit</b>, a Database of Drosophila Brain Neurons:<br />[http://www.flycircuit.tw/ FlyCircuit, National Tsing Hua University, Taiwan] |
| − | * FlyMove, an Image, Movie and Interactive Shockwave Resource:<br />[http://flymove.uni-muenster.de/ FlyMove, Muenster, Germany] | + | * <b>FlyMove</b>, an Image, Movie and Interactive Shockwave Resource:<br />[http://flymove.uni-muenster.de/ FlyMove, Muenster, Germany] |
| − | * FlyPNS, ''D. melanogaster'' embryonic and larval peripheral nervous system:<br />[http://www.normalesup.org/~vorgogoz/FlyPNS/page1.html FlyPNS, UMPC, Paris, France and Columbia University, NY, USA] | + | * <b>FlyPNS</b>, ''D. melanogaster'' embryonic and larval peripheral nervous system:<br />[http://www.normalesup.org/~vorgogoz/FlyPNS/page1.html FlyPNS, UMPC, Paris, France and Columbia University, NY, USA] |
| − | * FlyView, a Drosophila Image Database:<br />[http://flyview.uni-muenster.de/ FlyView, Muenster, Germany] | + | * <b>FlyView</b>, a Drosophila Image Database:<br />[http://flyview.uni-muenster.de/ FlyView, Muenster, Germany] |
| − | * GETDB, a Gal4 enhancer trap database:<br />[https://kyotofly.kit.jp/stocks/GETDB/getdb.html GETDB, Kyoto Institute of Technology, Kyoto, Japan] | + | * <b>GETDB</b>, a Gal4 enhancer trap database:<br />[https://kyotofly.kit.jp/stocks/GETDB/getdb.html GETDB, Kyoto Institute of Technology, Kyoto, Japan] |
| − | * Interactive Maps: four maps displaying markers and lineages of ''D. melanogaster'' neuroblasts, glial cells, and interneurons:<br />[http://www.genetik.biologie.uni-mainz.de/106.php Interactive Maps, Institut fur Genetik, Johannes Gutenberg University, Mainz, Germany] | + | * <b>Interactive Maps</b>: four maps displaying markers and lineages of ''D. melanogaster'' neuroblasts, glial cells, and interneurons:<br />[http://www.genetik.biologie.uni-mainz.de/106.php Interactive Maps, Institut fur Genetik, Johannes Gutenberg University, Mainz, Germany] |
| − | * Jove, videos of experimental techniques:<br />[http://www.jove.com/index/browse.stp?Search=Drosophila Jove, Journal of Visualized Experiments, USA] | + | * <b>Jove</b>, videos of experimental techniques:<br />[http://www.jove.com/index/browse.stp?Search=Drosophila Jove, Journal of Visualized Experiments, USA] |
| − | * Scans of Bridges' original 1935 polytene drawings for ''D. melanogaster''<nowiki>:</nowiki><br />[http://www.hawaii.edu/bio/Chromosomes/poly/poly.html GEM Website, University of Hawaii, USA] | + | * <b>Scans of Bridges</b>' original 1935 polytene drawings for ''D. melanogaster''<nowiki>:</nowiki><br />[http://www.hawaii.edu/bio/Chromosomes/poly/poly.html GEM Website, University of Hawaii, USA] |
| − | * Virtual Fly Brain - A 3D brain browser with point and click searches for neurons, transgenes and phenotypes:<br />[http://www.virtualflybrain.org Virtual Fly Brain, Edinburgh and Cambridge, UK] | + | * <b>Virtual Fly Brain</b> - A 3D brain browser with point and click searches for neurons, transgenes and phenotypes:<br />[http://www.virtualflybrain.org Virtual Fly Brain, Edinburgh and Cambridge, UK] |
=CRISPRs and TALENs= | =CRISPRs and TALENs= | ||
| − | * Cas9 Design:<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] |
| − | * CRISPR Efficiency Tool for Assessment of Designs:<br />[http://www.flyrnai.org/evaluateCrispr/ DRSC, Harvard Medical School, Boston, MA, USA] | + | * <b>CRISPR Efficiency Tool for Assessment of Designs</b>:<br />[http://www.flyrnai.org/evaluateCrispr/ DRSC, Harvard Medical School, Boston, MA, USA] |
| − | * CRISPR Genome Engineering Resources:<br />[http://www.genome-engineering.org/crispr/ Zhang lab, MIT, Boston, MA, USA] | + | * <b>CRISPR Genome Engineering Resources</b>:<br />[http://www.genome-engineering.org/crispr/ Zhang lab, MIT, Boston, MA, USA] |
| − | * CRISPR fly design -- reagents, protocols, and results from fly CRISPR/Cas experiments:<br />[http://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://http://www.crisprflydesign.org/ Bullolk Lab, MRC Laboratory of Molecular Biology, Cambridge, UK] |
| − | * E-CRISP, 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] |
| − | * E-TALEN, 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] |
| − | * Finding CRISPRs, Drosophila CRISPR gRNA design search tool:<br />[http://www.flyrnai.org/crispr2/ DRSC, Harvard Medical School, Boston, MA, USA] | + | * <b>Finding CRISPRs</b>, Drosophila CRISPR gRNA design search tool:<br />[http://www.flyrnai.org/crispr2/ DRSC, Harvard Medical School, Boston, MA, USA] |
| − | * flyCRISPR, 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] |
| − | * flyCRISPR, 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] |
| − | * Genome Engineering by CRISPR/Cas9 in Drosophila:<br />[http://www.shigen.nig.ac.jp/fly/nigfly/cas9/ NIG/FLY/Ueda lab, Mishima, Japan] | + | * <b>Genome Engineering by CRISPR/Cas9 in Drosophila</b>:<br />[http://www.shigen.nig.ac.jp/fly/nigfly/cas9/ NIG/FLY/Ueda lab, Mishima, Japan] |
| − | * Mojo Hand, A TALEN Design Tool:<br />[http://www.talendesign.org/ Ekker lab, Mayo Clinic, Rochester, MN, USA] | + | * <b>Mojo Hand</b>, A TALEN Design Tool:<br />[http://www.talendesign.org/ Ekker lab, Mayo Clinic, Rochester, MN, USA] |
| − | * OXfCRISPR, Oxford Fly CRISPR Resources:<br />[http://groups.mrcfgu.ox.ac.uk/liu-group/useful-links/oxfcrispr/oxfcrispr Liu lab, University of Oxford, Oxford, UK] | + | * <b>OXfCRISPR</b>, Oxford Fly CRISPR Resources:<br />[http://groups.mrcfgu.ox.ac.uk/liu-group/useful-links/oxfcrispr/oxfcrispr Liu lab, University of Oxford, Oxford, UK] |
| − | * SIFTED, Specificity Inference for TAL Effector Design:<br />[http://thebrain.bwh.harvard.edu/software.html Bulyk Lab, Harvard Medical School, Boston, MA, USA] | + | * <b>SIFTED</b>, Specificity Inference for TAL Effector Design:<br />[http://thebrain.bwh.harvard.edu/software.html Bulyk Lab, Harvard Medical School, Boston, MA, USA] |
| − | * TAL Effectors:<br />[http://taleffector.genome-engineering.org/ Zhang lab, MIT, Boston, MA, USA] | + | * <b>TAL Effectors</b>:<br />[http://taleffector.genome-engineering.org/ Zhang lab, MIT, Boston, MA, USA] |
| − | * TALengineering.org, A Comprehensive Resource for Engineered TAL Effector Technology:<br />[http://talengineering.org/ Ekker lab, Joung Lab, MGH, Boston, USA] | + | * <b>TALengineering.org</b>, A Comprehensive Resource for Engineered TAL Effector Technology:<br />[http://talengineering.org/ Ekker lab, Joung Lab, MGH, Boston, USA] |
| − | * ZiFiT Targeter, Tool for Identifying Zinc Finger Nuclease Sites in Specific Target Sequences:<br />[http://zifit.partners.org/ZiFiT/ MGH and Harvard Medical School, Boston, MA] | + | * <b>ZiFiT Targeter</b>, Tool for Identifying Zinc Finger Nuclease Sites in Specific Target Sequences:<br />[http://zifit.partners.org/ZiFiT/ MGH and Harvard Medical School, Boston, MA] |
=Data Repositories= | =Data Repositories= | ||
| − | * Array Express - Functional Genomics Data:<br />[http://www.ebi.ac.uk/arrayexpress/ Array Express, EMBL-EBI, Hinxton, UK] | + | * <b>Array Express</b> - Functional Genomics Data:<br />[http://www.ebi.ac.uk/arrayexpress/ Array Express, EMBL-EBI, Hinxton, UK] |
| − | * Berkeley Drosophila Genome Project (BDGP):<br />[http://www.fruitfly.org/ BDGP, University of California, Berkeley, USA] | + | * <b>Berkeley Drosophila Genome Project (BDGP)</b>:<br />[http://www.fruitfly.org/ BDGP, University of California, Berkeley, USA] |
| − | * DDBJ, the DNA Data Bank of Japan:<br />[http://www.ddbj.nig.ac.jp/ DDBJ, National Institute of Genetics, Mishima, Japan] | + | * <b>DDBJ</b>, the DNA Data Bank of Japan:<br />[http://www.ddbj.nig.ac.jp/ DDBJ, National Institute of Genetics, Mishima, Japan] |
| − | * EMBL-EBI, The European Bioinformatics Institute:<br />[http://www.ebi.ac.uk/ EMBL-EBI, Hinxton, UK] | + | * <b>EMBL-EBI</b>, The European Bioinformatics Institute:<br />[http://www.ebi.ac.uk/ EMBL-EBI, Hinxton, UK] |
| − | * ENA, European Nucleotide Archive:<br />[http://www.ebi.ac.uk/embl/ ENA, European Nucleotide Archive, EMBL-EBI, Hinxton, UK] | + | * <b>ENA</b>, European Nucleotide Archive:<br />[http://www.ebi.ac.uk/embl/ ENA, European Nucleotide Archive, EMBL-EBI, Hinxton, UK] |
| − | * Ensembl Genome Browser:<br />[http://useast.ensembl.org/index.html EMBL-EBI, Hinxton, UK] | + | * <b>Ensembl Genome Browser</b>:<br />[http://useast.ensembl.org/index.html EMBL-EBI, Hinxton, UK] |
| − | * GenBank,the NIH genetic sequence database:<br />[http://www.ncbi.nlm.nih.gov/Genbank/ GenBank, NCBI, Bethesda, MD USA] | + | * <b>GenBank</b>,the NIH genetic sequence database:<br />[http://www.ncbi.nlm.nih.gov/Genbank/ GenBank, NCBI, Bethesda, MD USA] |
| − | * GEO Datasets, Gene Expression Omnibus:<br />[http://www.ncbi.nlm.nih.gov/geo/info/datasets.html NCBI, Bethesda, MD USA] | + | * <b>GEO Datasets</b>, Gene Expression Omnibus:<br />[http://www.ncbi.nlm.nih.gov/geo/info/datasets.html NCBI, Bethesda, MD USA] |
| − | * NCBI, National Center fo Biotechnology Information:<br />[http://www.ncbi.nlm.nih.gov Bethesda, MD USA] | + | * <b>NCBI</b>, National Center fo Biotechnology Information:<br />[http://www.ncbi.nlm.nih.gov Bethesda, MD USA] |
| − | * PubMed, Biomedical literature full-text archive:<br />[http://www.ncbi.nlm.nih.gov/pubmed PubMed, NCBI, Bethesda, MD USA] | + | * <b>PubMed</b>, Biomedical literature full-text archive:<br />[http://www.ncbi.nlm.nih.gov/pubmed PubMed, NCBI, Bethesda, MD USA] |
| − | * PubMed Central, Biomedical literature citations and abstracts:<br />[http://www.ncbi.nlm.nih.gov/pmc/ PubMed Central, NCBI, Bethesda, MD USA] | + | * <b>PubMed Central</b>, Biomedical literature citations and abstracts:<br />[http://www.ncbi.nlm.nih.gov/pmc/ PubMed Central, NCBI, Bethesda, MD USA] |
| − | * SRA, Sequence Read Archive:<br />[http://www.ncbi.nlm.nih.gov/sra SRA, NCBI, Bethesda, MD, USA] | + | * <b>SRA</b>, Sequence Read Archive:<br />[http://www.ncbi.nlm.nih.gov/sra SRA, NCBI, Bethesda, MD, USA] |
| − | * UCSC Genome Browser Gateway - D. melanogaster:<br />[http://genome.ucsc.edu/cgi-bin/hgGateway UCSC Genome Browser, UC Santa Cruz, USA] | + | * <b>UCSC Genome Browser Gateway</b> - D. melanogaster:<br />[http://genome.ucsc.edu/cgi-bin/hgGateway UCSC Genome Browser, UC Santa Cruz, USA] |
=Data and Metadata for Drosophila Genomes= | =Data and Metadata for Drosophila Genomes= | ||
| − | * List of Drosophila reference genome assemblies at FlyBase, NCBI and UCSC. [[File:Drosophila_Genome_Assemblies.xls]] (spreadsheet) ''Updated June 17, 2015'' | + | * <b>List of Drosophila reference genome assemblies</b> at FlyBase, NCBI and UCSC. [[File:Drosophila_Genome_Assemblies.xls]] (spreadsheet) ''Updated June 17, 2015'' |
| − | * ''D. albomicans'' Genome:<br />[http://www.ncbi.nlm.nih.gov/genome/2712/ D. albomicans Organism Overview, NCBI, USA]<br />[http://www.ebi.ac.uk/ena/data/view/GCA_000298335 D. albomicans Genome Assembly Report, ENA, UK] | + | * <b>''D. albomicans'' Genome</b>:<br />[http://www.ncbi.nlm.nih.gov/genome/2712/ D. albomicans Organism Overview, NCBI, USA]<br />[http://www.ebi.ac.uk/ena/data/view/GCA_000298335 D. albomicans Genome Assembly Report, ENA, UK] |
| − | * ''D. ananassae'' Genome:<br />[http://www.ncbi.nlm.nih.gov/genome/244/ D. ananassae Organism Overview, NCBI, USA]<br />[http://www.ebi.ac.uk/ena/data/view/GCA_000005115 D. ananassae Genome Assembly Report, ENA, UK] | + | * <b>''D. ananassae'' Genome</b>:<br />[http://www.ncbi.nlm.nih.gov/genome/244/ D. ananassae Organism Overview, NCBI, USA]<br />[http://www.ebi.ac.uk/ena/data/view/GCA_000005115 D. ananassae Genome Assembly Report, ENA, UK] |
| − | * ''D. biarmipes'' Genome:<br />[http://www.ncbi.nlm.nih.gov/genome/3499/ D. biarmipes Organism Overview, NCBI, USA]<br />[http://www.ebi.ac.uk/ena/data/view/GCA_000233415 D. biarmipes Genome Assembly Report, ENA, UK] | + | * <b>''D. biarmipes'' Genome</b>:<br />[http://www.ncbi.nlm.nih.gov/genome/3499/ D. biarmipes Organism Overview, NCBI, USA]<br />[http://www.ebi.ac.uk/ena/data/view/GCA_000233415 D. biarmipes Genome Assembly Report, ENA, UK] |
| − | * ''D. bipectinata'' Genome:<br />[http://www.ncbi.nlm.nih.gov/genome/3489/ D. bipectinata Organism Overview, NCBI, USA]<br />[http://www.ebi.ac.uk/ena/data/view/GCA_000236285 D. bipectinata Genome Assembly Report, ENA, UK] | + | * <b>''D. bipectinata'' Genome</b>:<br />[http://www.ncbi.nlm.nih.gov/genome/3489/ D. bipectinata Organism Overview, NCBI, USA]<br />[http://www.ebi.ac.uk/ena/data/view/GCA_000236285 D. bipectinata Genome Assembly Report, ENA, UK] |
| − | * ''D. erecta'' Genome | + | * <b>''D. erecta'' Genome</b>:<br />[http://www.ncbi.nlm.nih.gov/genome/250/ D. erecta Organism Overview, NCBI, USA]<br />[http://www.ebi.ac.uk/ena/data/view/GCA_000005135 D. erecta Genome Assembly Report, ENA, UK] |
| − | * ''D. elegans'' Genome:<br />[http://www.ncbi.nlm.nih.gov/genome/3490 D. elegans Organism Overview, NCBI, USA]<br />[http://www.ebi.ac.uk/ena/data/view/GCA_000224195 D. elegans Genome Assembly Report, ENA, UK] | + | * <b>''D. elegans'' Genome</b>:<br />[http://www.ncbi.nlm.nih.gov/genome/3490 D. elegans Organism Overview, NCBI, USA]<br />[http://www.ebi.ac.uk/ena/data/view/GCA_000224195 D. elegans Genome Assembly Report, ENA, UK] |
| − | * ''D. eugracilis'' Genome:<br />[http://www.ncbi.nlm.nih.gov/genome/6863/ D. eugracilis Organism Overview, NCBI, USA]<br />[http://www.ebi.ac.uk/ena/data/view/GCA_000236325 D. eugracilis Genome Assembly Report, ENA, UK] | + | * <b>''D. eugracilis'' Genome</b>:<br />[http://www.ncbi.nlm.nih.gov/genome/6863/ D. eugracilis Organism Overview, NCBI, USA]<br />[http://www.ebi.ac.uk/ena/data/view/GCA_000236325 D. eugracilis Genome Assembly Report, ENA, UK] |
| − | * ''D. ficusphila'' Genome:<br />[http://www.ncbi.nlm.nih.gov/genome/3491/ D. ficusphila Organism Overview, NCBI, USA]<br />[http://www.ebi.ac.uk/ena/data/view/GCA_000220665 D. ficusphila Genome Assembly Report, ENA, UK] | + | * <b>''D. ficusphila'' Genome</b>:<br />[http://www.ncbi.nlm.nih.gov/genome/3491/ D. ficusphila Organism Overview, NCBI, USA]<br />[http://www.ebi.ac.uk/ena/data/view/GCA_000220665 D. ficusphila Genome Assembly Report, ENA, UK] |
| − | * ''D. grimshawi'' Genome:<br />[http://www.ncbi.nlm.nih.gov/genome/257/ D. grimshawi Organism Overview, NCBI, USA]<br />[http://www.ebi.ac.uk/ena/data/view/GCA_000005155 D. grimshawi Genome Assembly Report, ENA, UK] | + | * <b>''D. grimshawi'' Genome</b>:<br />[http://www.ncbi.nlm.nih.gov/genome/257/ D. grimshawi Organism Overview, NCBI, USA]<br />[http://www.ebi.ac.uk/ena/data/view/GCA_000005155 D. grimshawi Genome Assembly Report, ENA, UK] |
| − | * ''D. kikkawai'' Genome | + | * <b>''D. kikkawai'' Genome</b>:<br />[http://www.ncbi.nlm.nih.gov/genome/3492/ D. kikkawai Organism Overview, NCBI, USA]<br />[http://www.ebi.ac.uk/ena/data/view/GCA_000224215 D. kikkawai Genome Assembly Report, ENA, UK] |
| − | * ''D. melanogaster'' Genome:<br />[http://www.ncbi.nlm.nih.gov/genome/47/ D. melanogaster Organism Overview, NCBI, USA]<br />[http://www.ebi.ac.uk/ena/data/view/GCA_000001215 D. melanogaster Genome Assembly Report, ENA, UK] | + | * <b>''D. melanogaster'' Genome</b>:<br />[http://www.ncbi.nlm.nih.gov/genome/47/ D. melanogaster Organism Overview, NCBI, USA]<br />[http://www.ebi.ac.uk/ena/data/view/GCA_000001215 D. melanogaster Genome Assembly Report, ENA, UK] |
| − | * ''D. miranda'' Genome:<br />[http://www.ncbi.nlm.nih.gov/genome/10915/ D. miranda Organism Overview, NCBI, USA]<br />[http://www.ebi.ac.uk/ena/data/view/GCA_000269505 D. miranda Genome Assembly Report, ENA, UK] | + | * <b>''D. miranda'' Genome</b>:<br />[http://www.ncbi.nlm.nih.gov/genome/10915/ D. miranda Organism Overview, NCBI, USA]<br />[http://www.ebi.ac.uk/ena/data/view/GCA_000269505 D. miranda Genome Assembly Report, ENA, UK] |
| − | * ''D. mojavensis'' Genome:<br />[http://www.ncbi.nlm.nih.gov/genome/259/ D. mojavensis Organism Overview, NCBI, USA]<br />[http://www.ebi.ac.uk/ena/data/view/GCA_000005175 D. mojavensis Genome Assembly Report, ENA, UK] | + | * <b>''D. mojavensis'' Genome</b>:<br />[http://www.ncbi.nlm.nih.gov/genome/259/ D. mojavensis Organism Overview, NCBI, USA]<br />[http://www.ebi.ac.uk/ena/data/view/GCA_000005175 D. mojavensis Genome Assembly Report, ENA, UK] |
| − | * ''D. persimilis'' Genome:<br />[http://www.ncbi.nlm.nih.gov/genome/265/ D. persimilis Organism Overview, NCBI, USA]<br />[http://www.ebi.ac.uk/ena/data/view/GCA_000005195 D. persimilis Genome Assembly Report, ENA, UK] | + | * <b>''D. persimilis'' Genome</b>:<br />[http://www.ncbi.nlm.nih.gov/genome/265/ D. persimilis Organism Overview, NCBI, USA]<br />[http://www.ebi.ac.uk/ena/data/view/GCA_000005195 D. persimilis Genome Assembly Report, ENA, UK] |
| − | * ''D. pseudoobscura'' Genome | + | * <b>''D. pseudoobscura'' Genome</b>:<br />[http://www.ncbi.nlm.nih.gov/genome/219/ D. pseudoobscura Organism Overview, NCBI, USA]<br />[http://www.ebi.ac.uk/ena/data/view/GCA_000001765 D. pseudoobscura Genome Assembly Report, ENA, UK] |
| − | * ''D. rhopaloa'' Genome:<br />[http://www.ncbi.nlm.nih.gov/genome/6853/ D. rhopaloa Organism Overview, NCBI, USA]<br />[http://www.ebi.ac.uk/ena/data/view/GCA_000236305 D. rhopaloa Genome Assembly Report, ENA, UK] | + | * <b>''D. rhopaloa'' Genome</b>:<br />[http://www.ncbi.nlm.nih.gov/genome/6853/ D. rhopaloa Organism Overview, NCBI, USA]<br />[http://www.ebi.ac.uk/ena/data/view/GCA_000236305 D. rhopaloa Genome Assembly Report, ENA, UK] |
| − | * ''D. sechellia'' Genome:<br />[http://www.ncbi.nlm.nih.gov/genome/271/ D. sechellia Organism Overview, NCBI, USA]<br />[http://www.ebi.ac.uk/ena/data/view/GCA_000005215 D. sechellia Genome Assembly Report, ENA, UK] | + | * <b>''D. sechellia'' Genome</b>:<br />[http://www.ncbi.nlm.nih.gov/genome/271/ D. sechellia Organism Overview, NCBI, USA]<br />[http://www.ebi.ac.uk/ena/data/view/GCA_000005215 D. sechellia Genome Assembly Report, ENA, UK] |
| − | * ''D. simulans'' Genome:<br />[http://www.ncbi.nlm.nih.gov/genome/200/ D. simulans Organism Overview, NCBI, USA]<br />[http://www.ebi.ac.uk/ena/data/view/GCA_000259045 D. simulans Genome Assembly Report, ENA, UK] | + | * <b>''D. simulans'' Genome</b>:<br />[http://www.ncbi.nlm.nih.gov/genome/200/ D. simulans Organism Overview, NCBI, USA]<br />[http://www.ebi.ac.uk/ena/data/view/GCA_000259045 D. simulans Genome Assembly Report, ENA, UK] |
| − | * ''D. suzukii'' Genome:<br />[http://www.ncbi.nlm.nih.gov/genome/18317/ D. suzukii Organism Overview, NCBI, USA]<br />[http://www.ebi.ac.uk/ena/data/view/GCA_000472105 D. suzukii Genome Assembly Report, ENA, UK] | + | * <b>''D. suzukii'' Genome</b>:<br />[http://www.ncbi.nlm.nih.gov/genome/18317/ D. suzukii Organism Overview, NCBI, USA]<br />[http://www.ebi.ac.uk/ena/data/view/GCA_000472105 D. suzukii Genome Assembly Report, ENA, UK] |
| − | * ''D. takahashii'' Genome:<br />[http://www.ncbi.nlm.nih.gov/genome/3493/ D. takahashii Organism Overview, NCBI, USA]<br />[http://www.ebi.ac.uk/ena/data/view/GCA_000224235 D. takahashii Genome Assembly Report, ENA, UK] | + | * <b>''D. takahashii'' Genome</b>:<br />[http://www.ncbi.nlm.nih.gov/genome/3493/ D. takahashii Organism Overview, NCBI, USA]<br />[http://www.ebi.ac.uk/ena/data/view/GCA_000224235 D. takahashii Genome Assembly Report, ENA, UK] |
| − | * ''D. virilis'' Genome:<br />[http://www.ncbi.nlm.nih.gov/genome/261/ D. virilis Organism Overview, NCBI, USA]<br />[http://www.ebi.ac.uk/ena/data/view/GCA_000005245 D. virilis Genome Assembly Report, ENA, UK] | + | * <b>''D. virilis'' Genome</b>:<br />[http://www.ncbi.nlm.nih.gov/genome/261/ D. virilis Organism Overview, NCBI, USA]<br />[http://www.ebi.ac.uk/ena/data/view/GCA_000005245 D. virilis Genome Assembly Report, ENA, UK] |
| − | * ''D. willistoni'' Genome:<br />[http://www.ncbi.nlm.nih.gov/genome/251/ D. willistoni Organism Overview, NCBI, USA]<br />[http://www.ebi.ac.uk/ena/data/view/GCA_000005925 D. willistoni Genome Assembly Report, ENA, UK] | + | * <b>''D. willistoni'' Genome</b>:<br />[http://www.ncbi.nlm.nih.gov/genome/251/ D. willistoni Organism Overview, NCBI, USA]<br />[http://www.ebi.ac.uk/ena/data/view/GCA_000005925 D. willistoni Genome Assembly Report, ENA, UK] |
| − | * ''D. yakuba'' Genome:<br />[http://www.ncbi.nlm.nih.gov/genome/148/ D. yakuba Organism Overview, NCBI, USA]<br />[http://www.ebi.ac.uk/ena/data/view/GCA_000005975 D. yakuba Genome Assembly Report, ENA, UK]] | + | * <b>''D. yakuba'' Genome</b>:<br />[http://www.ncbi.nlm.nih.gov/genome/148/ D. yakuba Organism Overview, NCBI, USA]<br />[http://www.ebi.ac.uk/ena/data/view/GCA_000005975 D. yakuba Genome Assembly Report, ENA, UK]] |
=Genome Sequencing Projects= | =Genome Sequencing Projects= | ||
| − | * ''D. pseudoobscura'' genome project:<br />[https://www.hgsc.bcm.edu/arthropods/drosophila-pseudoobscura-genome-project D. pseudoobscura Human Genome Sequencing Center, Baylor College of Medicine, USA] | + | * <b>''D. pseudoobscura'' genome project</b>:<br />[https://www.hgsc.bcm.edu/arthropods/drosophila-pseudoobscura-genome-project D. pseudoobscura Human Genome Sequencing Center, Baylor College of Medicine, USA] |
| − | * ''D. simulans'' genome project:<br />[http://genome.wustl.edu/genomes/detail/drosophila-simulans-white-501/ D. simulans White 501 Genome Sequencing Center, Washington University, USA] | + | * <b>''D. simulans'' genome project</b>:<br />[http://genome.wustl.edu/genomes/detail/drosophila-simulans-white-501/ D. simulans White 501 Genome Sequencing Center, Washington University, USA] |
| − | * ''D. yakuba'' genome project:<br />[http://genome.wustl.edu/genomes/detail/drosophila-yakuba/ D. yakuba Genome Sequencing Center, Washington University, USA] | + | * <b>''D. yakuba'' genome project</b>:<br />[http://genome.wustl.edu/genomes/detail/drosophila-yakuba/ D. yakuba Genome Sequencing Center, Washington University, USA] |
| − | * D. simulans and yakuba sequencing projects:<br />[http://www.dpgp.org/sim_yak/index.html DPGP, University of California, Davis, USA] | + | * <b>D. simulans and yakuba sequencing projects:<br />[http://www.dpgp.org/sim_yak/index.html DPGP, University of California, Davis, USA] |
=Gene Expression Databases and Tools= | =Gene Expression Databases and Tools= | ||
| − | * BDGP in situ, 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] |
| − | * BDTNP, 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] |
| − | * DGRC, Cell Line Expression tool (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] |
| − | * DRSC, Cell Line Expression tool (based on modENCODE data):<br />[http://www.flyrnai.org/cgi-bin/RNAi_expression_levels.pl DRSC, Harvard Medical School, Boston, MA, USA] | + | * <b>DRSC, Cell Line Expression tool</b> (based on modENCODE data):<br />[http://www.flyrnai.org/cgi-bin/RNAi_expression_levels.pl DRSC, Harvard Medical School, Boston, MA, USA] |
| − | * FlyAnnotator, Annotation of Gene Expression:<br />[http://www.flyprot.org/index.php FlyAnnotator, University of Cambridge, UK] | + | * <b>FlyAnnotator</b>, Annotation of Gene Expression:<br />[http://www.flyprot.org/index.php FlyAnnotator, University of Cambridge, UK] |
| − | * FlyAtlas2, for exploring how genes are expressed in the tissues of ''D. melanogaster'':<br />[http://flyatlas.gla.ac.uk/flyatlas/index.html FlyAtlas2, University of Glasgow, Glasgow, UK] | + | * <b>FlyAtlas2</b>, for exploring how genes are expressed in the tissues of ''D. melanogaster'':<br />[http://flyatlas.gla.ac.uk/flyatlas/index.html FlyAtlas2, University of Glasgow, Glasgow, UK] |
| − | * FlyEx, a Database of Segmentation Gene Expression in Drosophila:<br />[http://urchin.spbcas.ru/flyex/ FlyEx, St. Petersburg State Polytechnical University, Russia] | + | * <b>FlyEx</b>, a Database of Segmentation Gene Expression in Drosophila:<br />[http://urchin.spbcas.ru/flyex/ FlyEx, St. Petersburg State Polytechnical University, Russia] |
| − | * FlyExpress, an Expression Pattern Search Engine:<br />[http://www.flyexpress.net/ FlyExpress, Arizona State University, USA] | + | * <b>FlyExpress</b>, an Expression Pattern Search Engine:<br />[http://www.flyexpress.net/ FlyExpress, Arizona State University, USA] |
| − | * Fly-FISH, A Database of Drosophila Embryo mRNA Localizaton Patterns:<br />[http://fly-fish.ccbr.utoronto.ca/ Fly-FISH, University of Toronto, Toronto, Canada] | + | * <b>Fly-FISH</b>, A Database of Drosophila Embryo mRNA Localizaton Patterns:<br />[http://fly-fish.ccbr.utoronto.ca/ Fly-FISH, University of Toronto, Toronto, Canada] |
| − | * FlyLight, 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] |
| − | * flytrap, 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] |
| − | * GEO Profiles, 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] |
| − | * RNAMiner, A Bioinformatics Protocol for Mining Large RNA-Seq Transcriptomics Data:<br />[http://calla.rnet.missouri.edu/rnaminer/ Cheng Lab, University of Missouri, Mizzou, Columbia, MO, USA] | + | * <b>RNAMiner</b>, A Bioinformatics Protocol for Mining Large RNA-Seq Transcriptomics Data:<br />[http://calla.rnet.missouri.edu/rnaminer/ Cheng Lab, University of Missouri, Mizzou, Columbia, MO, USA] |
=Gene Groups= | =Gene Groups= | ||
| − | * FlyBase Gene Group Reports:<br />[http://flybase.org/static_pages/feature/previous/articles/2015_05/gene_groups.html FlyBase Consortium] | + | * <b>FlyBase Gene Group Reports</b>:<br />[http://flybase.org/static_pages/feature/previous/articles/2015_05/gene_groups.html FlyBase Consortium] |
| − | * GLAD, 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] |
=General Bioinformatics Tools= | =General Bioinformatics Tools= | ||
| − | * Bioconductor, Open Source Software for Bioinformatics:<br />[http://www.bioconductor.org/ Fred Hutchinson Cancer Research Center, Seattle, USA] | + | * <b>Bioconductor</b>, Open Source Software for Bioinformatics:<br />[http://www.bioconductor.org/ Fred Hutchinson Cancer Research Center, Seattle, USA] |
| − | * BioMart, 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] |
| − | * Cytoscape - 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] |
| − | * DAVID (NIH) - Database for Annotation , Visualization and Integrated Discovery:<br />[http://david.abcc.ncifcrf.gov/ DAVID, NIH, Bethesda, MD, USA] | + | * <b>DAVID (NIH)</b> -- Database for Annotation , Visualization and Integrated Discovery:<br />[http://david.abcc.ncifcrf.gov/ DAVID, NIH, Bethesda, MD, USA] |
| − | * FlyMine, 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] |
| − | * FlyNet, a network prioritization server for Drosophila melanogaster biology:<br />[http://www.inetbio.org/flynet/ NetBioLab, Yonsei University, Seoul, Korea] | + | * <b>FlyNet</b>, a network prioritization server for Drosophila melanogaster biology:<br />[http://www.inetbio.org/flynet/ NetBioLab, Yonsei University, Seoul, Korea] |
| − | * Galaxy: 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] |
| − | * GSEA, 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] |
| − | * GOrilla - Gene Ontology enRIchment and anaLysis and viuaLizAtion tool:<br />[http://cbl-gorilla.cs.technion.ac.il/ GOrilla, Israel] | + | * <b>GOrilla</b> -- Gene Ontology enRIchment and anaLysis and viuaLizAtion tool:<br />[http://cbl-gorilla.cs.technion.ac.il/ GOrilla, Israel] |
=Human Disease: Drosophila Models and Orthologous Genes= | =Human Disease: Drosophila Models and Orthologous Genes= | ||
| − | * Bloomington Stock Center, Drosophila and Human Disease page:<br />[http://flystocks.bio.indiana.edu/Browse/HD/HDintro.htm Bloomington Stock Center, Bloomington, IN, USA] | + | * <b>Bloomington Stock Center</b>, Drosophila and Human Disease page:<br />[http://flystocks.bio.indiana.edu/Browse/HD/HDintro.htm Bloomington Stock Center, Bloomington, IN, USA] |
| − | * DIOPT-DIST, Disease-related Ortholog Tool:<br />[http://www.flyrnai.org/cgi-bin/DRSC_DG_query.pl DRSC, Harvard Medical School, Boston, MA, USA] | + | * <b>DIOPT-DIST</b>, Disease-related Ortholog Tool:<br />[http://www.flyrnai.org/cgi-bin/DRSC_DG_query.pl DRSC, Harvard Medical School, Boston, MA, USA] |
| − | * FlyNet Human Disease Prioritization: <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] |
| − | * HuDis, 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] |
=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] | + | * <b>BioGRID</b>, 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] | + | * <b>COMPLEAT</b>, 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] | + | * <b>DPiM</b>, 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] | + | * <b>DroID</b>, Drosophila Interactions Database:<br />[http://www.droidb.org/ Drosophila Interaction Database, Detroit, USA] |
| − | * Drosophila PIMRider, Drosophila Protein Interaction Map:<br />[https://pimr.hybrigenics.com/htmlFiles/interactionData/drosophila.html Drosophila PIMRider, Hybrigenics, Paris, France] | + | * <b>Drosophila PIMRider</b>, Drosophila Protein Interaction Map:<br />[https://pimr.hybrigenics.com/htmlFiles/interactionData/drosophila.html Drosophila PIMRider, Hybrigenics, Paris, France] |
| − | * FlyCyc - 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] |
| − | * FlyNet Gene Prioritization: <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] |
| − | * FlyReactome - 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] |
| − | * IM Browser, 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] |
| − | * IntAct, Molecular Interaction Database:<br />[http://www.ebi.ac.uk/intact/ IntAct, EMBL-EBI, Hinxton, UK] | + | * <b>IntAct</b>, Molecular Interaction Database:<br />[http://www.ebi.ac.uk/intact/ IntAct, EMBL-EBI, Hinxton, UK] |
| − | * KEGG - 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] |
| − | * Reactome Pathway Database:<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] |
| − | * SignedPPI, 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] |
| − | * STRING, 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] |
=miRNA and ncRNA Databases and Tools= | =miRNA and ncRNA Databases and Tools= | ||
| − | * DIANA microT-CDS, MicroRNA Target Prediction:<br />[http://diana.imis.athena-innovation.gr/DianaTools/ DIANA microT-CDS, DIANA LAB, Athens, Greece] | + | * <b>DIANA microT-CDS</b>, MicroRNA Target Prediction:<br />[http://diana.imis.athena-innovation.gr/DianaTools/ DIANA microT-CDS, DIANA LAB, Athens, Greece] |
| − | * DIANA TarBase, MicroRNA Target Database:<br />[http://diana.imis.athena-innovation.gr/DianaTools/ DIANA TarBase,, 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] |
| − | * MinoTar, 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>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] |
| − | * miRBase, microRNA data:<br />[http://www.mirbase.org/ miRBase, University of Manchester, UK] | + | * <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. | ::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:<br />[http://www.mirna.embl.de/ miRNA - Target Prediction, EMBL, Heidelberg, Germany] | + | * <b>miRNA, Target Gene Prediction</b>:<br />[http://www.mirna.embl.de/ miRNA - Target Prediction, EMBL, Heidelberg, Germany] |
| − | * miRNA_Targets:<br />[http://mamsap.it.deakin.edu.au/~amitkuma/mirna_targetsnew/index.html miRNA targets on full length mRNAs, Deakin University, Victoria, Australia] | + | * <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] |
| − | * miRTarBase, Experimentally Validated microRNA-target Interactions Database:<br />[http://mirtarbase.mbc.nctu.edu.tw/ miRTarBase, ISBLab, Hsinchu, Taiwan] | + | * <b>miRTarBase</b>, Experimentally Validated microRNA-target Interactions Database:<br />[http://mirtarbase.mbc.nctu.edu.tw/ miRTarBase, ISBLab, Hsinchu, Taiwan] |
| − | * Rfam, 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>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] |
| − | * TargetScanFly, Prediction of microRNA targets:<br />[http://www.targetscan.org/fly_12/ TargetScanFly, Whitehead Institute and MIT Dept. of Biology, 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= | ||
| − | * DOR, Database of Olfactory Receptors:<br />[http://caps.ncbs.res.in/DOR/index.html DOR, NCBS, Bangalore, India, AIST, Tokyo, Japan] | + | * <b>DOR</b>, Database of Olfactory Receptors:<br />[http://caps.ncbs.res.in/DOR/index.html DOR, NCBS, Bangalore, India, AIST, Tokyo, Japan] |
| − | * Drosophila Information Service:<br />[http://www.ou.edu/journals/dis/ DIS, Norman, Oklahoma, USA] | + | * <b>Drosophila Information Service</b>:<br />[http://www.ou.edu/journals/dis/ DIS, Norman, Oklahoma, USA] |
| − | * FlyTree, the Drosophila Researcher Genealogy has been incorporated into the Academic Tree Project: <br />[http://www.academictree.org/flytree/ FlyTree, USA] | + | * <b>FlyTree</b>, the Drosophila Researcher Genealogy has been incorporated into the Academic Tree Project: <br />[http://www.academictree.org/flytree/ FlyTree, USA] |
| − | * GenAge - 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] |
| − | * Gene Lookup, 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] |
| − | * Interactive Fly, 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] |
| − | * Jfly , 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] |
| − | * Manchester Fly Facility, Outreach resources - A compendium of information on ''Drosophila melanogaster'' as a model organism:<br />[http://www.flyfacility.ls.manchester.ac.uk/forthepublic/outreachresources/ University of Manchester, Manchester, UK] | + | * <b>Manchester Fly Facility, Outreach resources</b> - A compendium of information on ''Drosophila melanogaster'' as a model organism:<br />[http://www.flyfacility.ls.manchester.ac.uk/forthepublic/outreachresources/ University of Manchester, Manchester, UK] |
| − | * MitoDrome, ''Drosophila melanogaster'' nuclear genes encoding for mitochondrial proteins:<br />[http://mitodrome.ba.itb.cnr.it/ MitoDrome, Bari, Italy] | + | * <b>MitoDrome</b>, ''Drosophila melanogaster'' nuclear genes encoding for mitochondrial proteins:<br />[http://mitodrome.ba.itb.cnr.it/ MitoDrome, Bari, Italy] |
| − | * Mitotic Spindle Assembly Database:<br />[http://rnai.ucsf.edu/mitospindlescreen/index.html Genes Required for Mitotic Spindle Assembly in S2 cells, University of California, San Francisco, USA] | + | * <b>Mitotic Spindle Assembly Database:<br />[http://rnai.ucsf.edu/mitospindlescreen/index.html Genes Required for Mitotic Spindle Assembly in S2 cells, University of California, San Francisco, USA] |
| − | * PhenomicDB, A Cross-species Genotype-Phenotype Resource:<br />[http://phenomicdb.de/ Phenotype-Genotype Database, Berlin, Germany] | + | * <b>PhenomicDB</b>, A Cross-species Genotype-Phenotype Resource:<br />[http://phenomicdb.de/ Phenotype-Genotype Database, Berlin, Germany] |
| − | * PhospoPep - phosphorylation site data from ''D. melanogaster'' cell lines:<br />[http://www.phosphopep.org/ The Aebersold group at the ETH in collaboration with the FGCZ in Switzerland, and the ISB, USA.] | + | * <b>PhospoPep</b> -- phosphorylation site data from ''D. melanogaster'' cell lines:<br />[http://www.phosphopep.org/ The Aebersold group at the ETH in collaboration with the FGCZ in Switzerland, and the ISB, USA.] |
| − | * The WWW Virtual Library--Drosophila:<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] |
=Phylogenetic Comparison Tools= | =Phylogenetic Comparison Tools= | ||
| − | * Assembly/Alignment/Annotation of 12 related Drosophila species:<br />[http://rana.lbl.gov/drosophila/ Assembly/Alignment/Annotation, LBNL, USA] | + | * <b>Assembly/Alignment/Annotation of 12 related Drosophila species</b>:<br />[http://rana.lbl.gov/drosophila/ Assembly/Alignment/Annotation, LBNL, USA] |
| − | * DIOPT, 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] |
| − | * EvoPrinter, 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] |
| − | * InParanoid, 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] |
| − | * MANTiS 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] |
| − | * NCBI HomoloGene - automated system fo constructing putative homology groups:<br />[http://www.ncbi.nlm.nih.gov/homologene NCBI, Bethesda, MA, USA] | + | * <b>NCBI HomoloGene</b> -- automated system fo constructing putative homology groups:<br />[http://www.ncbi.nlm.nih.gov/homologene NCBI, Bethesda, MA, USA] |
| − | * OrthoDB, 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] |
| − | * Vista Tools - 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] |
=Population Biology and Polymorphism Resources= | =Population Biology and Polymorphism Resources= | ||
| − | * BDGP Single Nucleotide Polymorphism (SNP) Project:<br />[http://www.fruitfly.org/SNP/ Berkeley Drosophila Genome Project, University of California, Berkeley, USA] | + | * <b>BDGP Single Nucleotide Polymorphism (SNP) Project</b>:<br />[http://www.fruitfly.org/SNP/ Berkeley Drosophila Genome Project, University of California, Berkeley, USA] |
| − | * Drosophila Genetics Reference Panel:<br />[https://www.hgsc.bcm.edu/arthropods/drosophila-genetic-reference-panel DGRP, Baylor College of Medicine, Houston, TX and NC State University, Raleigh, NC USA] | + | * <b>Drosophila Genetics Reference Panel</b>:<br />[https://www.hgsc.bcm.edu/arthropods/drosophila-genetic-reference-panel DGRP, Baylor College of Medicine, Houston, TX and NC State University, Raleigh, NC USA] |
| − | * Drosophila Genetics Reference Panel 2:<br />[http://dgrp2.gnets.ncsu.edu/ DGRP2, NC State University, Raleigh, NC and Baylor College of Medicine, Houston, TX, USA] | + | * <b>Drosophila Genetics Reference Panel 2</b>:<br />[http://dgrp2.gnets.ncsu.edu/ DGRP2, NC State University, Raleigh, NC and Baylor College of Medicine, Houston, TX, USA] |
| − | * Drosophila Polymorphism Database:<br />[http://dgrp2.gnets.ncsu.edu/ DGRP2, Univ. Autònoma de Barcelona, Spain] | + | * <b>Drosophila Polymorphism Database</b>:<br />[http://dgrp2.gnets.ncsu.edu/ DGRP2, Univ. Autònoma de Barcelona, Spain] |
| − | * DPGP, Drosophila Population Genomics Project:<br />[http://www.dpgp.org/ DPGP, University of California, Davis, USA] | + | * <b>DPGP</b>, Drosophila Population Genomics Project:<br />[http://www.dpgp.org/ DPGP, University of California, Davis, USA] |
| − | * DSPR, Drosophila Synthetic Population Resource:<br />[http://wfitch.bio.uci.edu/~dspr/index.html DSPR, University of Kansas and UC Irvine, USA] | + | * <b>DSPR</b>, Drosophila Synthetic Population Resource:<br />[http://wfitch.bio.uci.edu/~dspr/index.html DSPR, University of Kansas and UC Irvine, USA] |
| − | * FlySNP Project:<br />[http://flysnp.imp.univie.ac.at/ FlySNP, Austrian Academy of Sciences, Austria] | + | * <b>FlySNP Project</b>:<br />[http://flysnp.imp.univie.ac.at/ FlySNP, Austrian Academy of Sciences, Austria] |
| − | * FlyVar Project: A Database of Drosophila Genetics Variations <br />[http://www.iipl.fudan.edu.cn/FlyVar/ FlyVar, Fudan University, Shanghai, China and Baylor College of Medicine, Houston, TX, USA] | + | * <b>FlyVar Project</b>: A Database of Drosophila Genetics Variations <br />[http://www.iipl.fudan.edu.cn/FlyVar/ FlyVar, Fudan University, Shanghai, China and Baylor College of Medicine, Houston, TX, USA] |
=Protein Analysis= | =Protein Analysis= | ||
| − | * GPCRDB, 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] |
| − | * InterPro protein domain analysis of Drosophila:<br />[http://www.ebi.ac.uk/interpro/ InterPro: protein sequence analysis & classification, EBI, UK] | + | * <b>InterPro protein domain analysis of Drosophila</b>:<br />[http://www.ebi.ac.uk/interpro/ InterPro: protein sequence analysis & classification, EBI, UK] |
| − | * MEROPS, 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] |
| − | * Panther protein classification system:<br />[http://panther.appliedbiosystems.com/about.jsp Panther Protein Classification System, Applied Biosystems & Celera, USA] | + | * <b>Panther protein classification system</b>:<br />[http://panther.appliedbiosystems.com/about.jsp Panther Protein Classification System, Applied Biosystems & Celera, USA] |
| − | * PDB, 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] |
| − | * SMART, Simple Modular Architecture Research Tool:<br />[http://smart.embl-heidelberg.de/ SMART, Protein Domain Analysis, EMBL, Heidleberg] | + | * <b>SMART</b>, Simple Modular Architecture Research Tool:<br />[http://smart.embl-heidelberg.de/ SMART, Protein Domain Analysis, EMBL, Heidleberg] |
| − | * UniProtKB, a comprehensive catalog of information on proteins:<br />[http://www.pir.uniprot.org/ UniProtKB, The UniProt Consortium] | + | * <b>UniProtKB</b>, a comprehensive catalog of information on proteins:<br />[http://www.pir.uniprot.org/ UniProtKB, The UniProt Consortium] |
=Public Education= | =Public Education= | ||
| − | * droso4schools, An online resource for school lessons using the fruit fly Drosophila:<br />[https://droso4schools.wordpress.com/ Manchester Fly Facility, University of Manchester, UK] | + | * <b>droso4schools</b>, An online resource for school lessons using the fruit fly Drosophila:<br />[https://droso4schools.wordpress.com/ Manchester Fly Facility, University of Manchester, UK] |
| − | * Fly on the Wall, a blog by Bethany Christmann regarding fruit flies and research:<br />[http://blogs.brandeis.edu/flyonthewall/ Griffith Lab, Brandeis University, Waltham, MA, USA] | + | * <b>Fly on the Wall</b>, a blog by Bethany Christmann regarding fruit flies and research:<br />[http://blogs.brandeis.edu/flyonthewall/ Griffith Lab, Brandeis University, Waltham, MA, USA] |
| − | * FlyMove, an Image, Movie and Interactive Shockwave Resource:<br />[http://flymove.uni-muenster.de/ FlyMove, Muenster, Germany] | + | * <b>FlyMove</b>, an Image, Movie and Interactive Shockwave Resource:<br />[http://flymove.uni-muenster.de/ FlyMove, Muenster, Germany] |
| − | * Manchester Fly Facility Public Resource Page:<br />[http://www.flyfacility.ls.manchester.ac.uk/forthepublic/ Manchester Fly Facility, University of Manchester, UK] | + | * <b>Manchester Fly Facility Public Resource Page</b>:<br />[http://www.flyfacility.ls.manchester.ac.uk/forthepublic/ Manchester Fly Facility, University of Manchester, UK] |
=RNAi= | =RNAi= | ||
| − | * DRSC, Drosophila RNAi Screening Center:<br />[http://www.flyrnai.org/index.html DRSC, Harvard Medical School, Boston, MA, USA] | + | * <b>DRSC</b>, Drosophila RNAi Screening Center:<br />[http://www.flyrnai.org/index.html DRSC, Harvard Medical School, Boston, MA, USA] |
| − | * Search by gene(s) to find hits in DRSC screens:<br /> [http://www.flyrnai.org/RNAi_find_hit_info.html DRSC, Harvard Medical School, Boston, MA, USA] | + | * <b>Search by gene(s) to find hits in DRSC screens</b>:<br /> [http://www.flyrnai.org/RNAi_find_hit_info.html DRSC, Harvard Medical School, Boston, MA, USA] |
| − | * Fosmid rescue analysis tool for identification of fosmids appropriate for cross-species rescue of RNAi:<br />[http://www.flyrnai.org/cgi-bin/RNAi_find_rescue_compl.pl DRSC, Harvard Medical School, Boston, MA, USA] | + | * <b>Fosmid rescue analysis tool</b> for identification of fosmids appropriate for cross-species rescue of RNAi:<br />[http://www.flyrnai.org/cgi-bin/RNAi_find_rescue_compl.pl DRSC, Harvard Medical School, Boston, MA, USA] |
| − | * GenomeRNAi, Heidelberg, a database of RNA interference (RNAi) screens in cultured Drosophila cells:<br />[http://www.dkfz.de/signaling2/rnai/index.php GenomeRNAi, DKFZ, Heidelberg, Germany] | + | * <b>GenomeRNAi</b>, Heidelberg, a database of RNA interference (RNAi) screens in cultured Drosophila cells:<br />[http://www.dkfz.de/signaling2/rnai/index.php GenomeRNAi, DKFZ, Heidelberg, Germany] |
| − | * GESS, off-target RNAi prediction:<br />[http://www.flyrnai.org/gess/ DRSC, Harvard Medical School, Boston, MA, USA] | + | * <b>GESS</b>, off-target RNAi prediction:<br />[http://www.flyrnai.org/gess/ DRSC, Harvard Medical School, Boston, MA, USA] |
| − | * Predicted Off-Target Free Sequence Regions:<br />[http://www.flyrnai.org/RNAi_find_frag_free.html DRSC, Harvard Medical School, Boston, MA, USA] | + | * <b>Predicted Off-Target Free Sequence Regions</b>:<br />[http://www.flyrnai.org/RNAi_find_frag_free.html DRSC, Harvard Medical School, Boston, MA, USA] |
| − | * RNAiCut, Automated Detection of Significant Genes from Functional Genomic Screens:<br /> [http://rnaicut.csail.mit.edu/ Berger Lab, MIT, Boston, MA, USA] | + | * <b>RNAiCut</b>, Automated Detection of Significant Genes from Functional Genomic Screens:<br /> [http://rnaicut.csail.mit.edu/ Berger Lab, MIT, Boston, MA, USA] |
| − | * RSVP, RNAi Stock Validation & Phenotypes:<br />[http://www.flyrnai.org/RSVP DRSC, Harvard Medical School, Boston, MA, USA] | + | * <b>RSVP</b>, RNAi Stock Validation & Phenotypes:<br />[http://www.flyrnai.org/RSVP DRSC, Harvard Medical School, Boston, MA, USA] |
| − | * SnapDragon, RNAi Design:<br />[http://www.flyrnai.org/cgi-bin/RNAi_find_primers.pl DRSC, Harvard Medical School, Boston, MA, USA] | + | * <b>SnapDragon</b>, RNAi Design:<br />[http://www.flyrnai.org/cgi-bin/RNAi_find_primers.pl DRSC, Harvard Medical School, Boston, MA, USA] |
| − | * TRiP, Transgenic RNAi Project: <br />[http://www.flyrnai.org/TRiP-HOME.html Transgenic RNAi Project, DRSC, Harvard Medical School, Boston, MA,USA] | + | * <b>TRiP</b>, Transgenic RNAi Project: <br />[http://www.flyrnai.org/TRiP-HOME.html Transgenic RNAi Project, DRSC, Harvard Medical School, Boston, MA,USA] |
| − | * Tsinghua Fly Center, Transgenic RNAi lines: <br />[http://center.biomed.tsinghua.edu.cn/public/eq-category/modelanimalfacility/ Center of Biomedical Analysis, Tsinghua University, Beijing, China] | + | * <b>Tsinghua Fly Center</b>, Transgenic RNAi lines: <br />[http://center.biomed.tsinghua.edu.cn/public/eq-category/modelanimalfacility/ Center of Biomedical Analysis, Tsinghua University, Beijing, China] |
| − | * UP-TORR Fly, a tool for identifying updated targets of RNAi reagents: <br />[http://www.flyrnai.org/up-torr/ Updated Targets of RNAi Reagents, DRSC, Harvard Medical School, Boston, MA,USA] | + | * <b>UP-TORR Fly</b>, a tool for identifying updated targets of RNAi reagents: <br />[http://www.flyrnai.org/up-torr/ Updated Targets of RNAi Reagents, DRSC, Harvard Medical School, Boston, MA,USA] |
| − | * VDRC, Vienna Drosophila Resource Center: <br />[http://stockcenter.vdrc.at/control/main Genome-wide transgenic Drosophila RNAi libraries, VDRC, Vienna, Austria] | + | * <b>VDRC</b>, Vienna Drosophila Resource Center: <br />[http://stockcenter.vdrc.at/control/main Genome-wide transgenic Drosophila RNAi libraries, VDRC, Vienna, Austria] |
=Sequence Analysis= | =Sequence Analysis= | ||
| − | * FlyPrimerBank, a comprehensive qPCR primer database for Drosophila: <br />[http://www.flyrnai.org/FlyPrimerBank FlyPrimerBank, DRSC, Harvard Medical School, Boston, MA, USA] | + | * <b>FlyPrimerBank</b>, a comprehensive qPCR primer database for Drosophila: <br />[http://www.flyrnai.org/FlyPrimerBank FlyPrimerBank, DRSC, Harvard Medical School, Boston, MA, USA] |
| − | * FGENESH, Annotation of animal genomes-genes, promoters, functional motifs, protein sub-cellular localization.:<br />[http://www.softberry.com/berry.phtml?topic=case_study_animal&no_menu=on Annotation of genomes, Softberry, USA] | + | * <b>FGENESH</b>, Annotation of animal genomes-genes, promoters, functional motifs, protein sub-cellular localization.:<br />[http://www.softberry.com/berry.phtml?topic=case_study_animal&no_menu=on Annotation of genomes, Softberry, USA] |
| − | * GenePalette, a tool for genome sequence visualization and navigation: <br />[http://www.genepalette.org/ GenePalette, University of California, San Diego, USA] | + | * <b>GenePalette</b>, a tool for genome sequence visualization and navigation: <br />[http://www.genepalette.org/ GenePalette, University of California, San Diego, USA] |
| − | * Genie Gene finder for Drosophila:<br />[http://www.fruitfly.org/seq_tools/genie.html Genie, Berkeley Drosophila Genome Project, University of California, Berkeley, USA] | + | * <b>Genie Gene finder for Drosophila</b>:<br />[http://www.fruitfly.org/seq_tools/genie.html Genie, Berkeley Drosophila Genome Project, University of California, Berkeley, USA] |
| − | * HRMA - High Resolution Melt Analysis: <br /> [http://www.flyrnai.org/hrma HRMA, DRSC, Harvard Medical School, Boston, MA, USA] | + | * <b>HRMA</b> -- High Resolution Melt Analysis: <br /> [http://www.flyrnai.org/hrma HRMA, DRSC, Harvard Medical School, Boston, MA, USA] |
| − | * MEME Suite - Motif-based Sequence Analysis Tools:<br />[http://meme.nbcr.net/meme/intro.html MEME, U. of Queensland, U. of Washington, USA, UCSD, SDSC, NBCR, CBRC, and National Center for Research Resources] | + | * <b>MEME Suite</b> -- Motif-based Sequence Analysis Tools:<br />[http://meme.nbcr.net/meme/intro.html MEME, U. of Queensland, U. of Washington, USA, UCSD, SDSC, NBCR, CBRC, and National Center for Research Resources] |
| − | * RepeatMasker: <br />[http://www.repeatmasker.org/ RepeatMasker Institute for Systems Biology, Seattle, WA, USA] | + | * <b>RepeatMasker</b>: <br />[http://www.repeatmasker.org/ RepeatMasker Institute for Systems Biology, Seattle, WA, USA] |
| − | * Splice Site Prediction for Drosophila:<br />[http://www.fruitfly.org/seq_tools/splice.html Splice Site Prediction, Berkeley Drosophila Genome Project, University of California, Berkeley, USA] | + | * <b>Splice Site Prediction for Drosophila</b>:<br />[http://www.fruitfly.org/seq_tools/splice.html Splice Site Prediction, Berkeley Drosophila Genome Project, University of California, Berkeley, USA] |
| − | * Web Apollo, a collaborative genomic annotation editor: <br />[http://apollo.berkeleybop.org/ Web Apollo, LBL, Berkeley, USA] | + | * <b>Web Apollo</b>, a collaborative genomic annotation editor: <br />[http://apollo.berkeleybop.org/ Web Apollo, LBL, Berkeley, USA] |
=Taxonomy= | =Taxonomy= | ||
| − | * Drosophilidae Taxonomic Database:<br />[http://bioinfo.lowtem.hokudai.ac.jp/db/modules/stdb/ Drosophilidae Taxonomic Database, Japan] | + | * <b>Drosophilidae Taxonomic Database</b>:<br />[http://bioinfo.lowtem.hokudai.ac.jp/db/modules/stdb/ Drosophilidae Taxonomic Database, Japan] |
| − | * Drosophilidae Taxonomy - Collection of Papers:<br />[http://www.dgrc.kit.ac.jp/~jdd/class/index.html Japan Drosophila Database (JDD) on Taxonomy, Japan] | + | * <b>Drosophilidae Taxonomy</b> -- Collection of Papers:<br />[http://www.dgrc.kit.ac.jp/~jdd/class/index.html Japan Drosophila Database (JDD) on Taxonomy, Japan] |
| − | * FlyPhenomics, phenotypic differences between species of the ''D. melanogaster'' subgroup:<br />[http://www.normalesup.org/~vorgogoz/FlyPhenomics/ FlyPhenomics, Paris, France] | + | * <b>FlyPhenomics</b>, phenotypic differences between species of the ''D. melanogaster'' subgroup:<br />[http://www.normalesup.org/~vorgogoz/FlyPhenomics/ FlyPhenomics, Paris, France] |
| − | * TaxoDros, the database on Taxonomy of Drosophilidae:<br />[http://www.taxodros.uzh.ch/ TaxoDros, University of Zurich, Switzerland] | + | * <b>TaxoDros</b>, the database on Taxonomy of Drosophilidae:<br />[http://www.taxodros.uzh.ch/ TaxoDros, University of Zurich, Switzerland] |
| − | * Taxonomy, NCBI Taxonomy Database:<br />[http://www.ncbi.nlm.nih.gov/taxonomy NCBI, Bethesda, MD USA] | + | * <b>Taxonomy</b>, NCBI Taxonomy Database:<br />[http://www.ncbi.nlm.nih.gov/taxonomy NCBI, Bethesda, MD USA] |
=Transcription Regulation Databases and Tools= | =Transcription Regulation Databases and Tools= | ||
| − | * BDTNP, ChIP/chip in vivo DNA binding data:<br />[http://bdtnp.lbl.gov/Fly-Net/chipchip.jsp?w=summary Berkeley Drosophila Transcription Network Project, University of California, Berkeley, USA] | + | * <b>BDTNP</b>, ChIP/chip in vivo DNA binding data:<br />[http://bdtnp.lbl.gov/Fly-Net/chipchip.jsp?w=summary Berkeley Drosophila Transcription Network Project, University of California, Berkeley, USA] |
| − | * cis-analyst, to search the Drosophila genome for clusters of binding sites: <br />[http://rana.lbl.gov/cis-analyst/ cis-analyst, Berkeley, USA] | + | * <b>cis-analyst</b>, to search the Drosophila genome for clusters of binding sites: <br />[http://rana.lbl.gov/cis-analyst/ cis-analyst, Berkeley, USA] |
| − | * DBD: Transcription factor prediction database: <br />[http://www.transcriptionfactor.org/index.cgi?Home DBD, MRC, Cambridge, UK] | + | * <b>DBD</b>: Transcription factor prediction database: <br />[http://www.transcriptionfactor.org/index.cgi?Home DBD, MRC, Cambridge, UK] |
| − | * DNase I Footprint Database:<nowiki>: </nowiki><br />[http://www.flyreg.org/ University of Manchester Bioinformatics Resources, University of Manchester, UK] | + | * <b>DNase I Footprint Database</b>:<nowiki>: </nowiki><br />[http://www.flyreg.org/ University of Manchester Bioinformatics Resources, University of Manchester, UK] |
| − | * EPD, the Eukaryotic Promoter Database:<br />[http://www.epd.isb-sib.ch/ EPD, Epalinges s/Lausanne, Switzerland] | + | * <b>EPD</b>, the Eukaryotic Promoter Database:<br />[http://www.epd.isb-sib.ch/ EPD, Epalinges s/Lausanne, Switzerland] |
| − | * Fly Factor Survey - Database of Drosophila TF DNA-binding Specificitiies: <br />[http://pgfe.umassmed.edu/ffs/ FLy Factor Survey, UMass Medical School, Worcester, MA, USA] | + | * <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] |
| − | * OnTheFly, 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] |
| − | * Neural Network Promoter Prediction for Drosophila:<br />[http://www.fruitfly.org/seq_tools/promoter.html Neural Network Promoter Prediction, Berkeley Drosophila Genome Project, University of California, Berkeley, USA] | + | * <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] |
| − | * PREdictor, 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] |
| − | * REDfly, 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] |
| − | * The Drosophila Transcription Factor Database:<br />[http://www.flytf.org/ FlyTF.org, MRC Cambridge, UK] | + | * <b>The Drosophila Transcription Factor Database</b>:<br />[http://www.flytf.org/ FlyTF.org, MRC Cambridge, UK] |
| − | * TRANSFAC, A database of transcription factors and their binding sites:<br />[http://www.gene-regulation.com/pub/databases.html#transfac TRANSFAC, Braunschweig, Germany] | + | * <b>TRANSFAC</b>, A database of transcription factors and their binding sites:<br />[http://www.gene-regulation.com/pub/databases.html#transfac TRANSFAC, Braunschweig, Germany] |
=Suggest a tool or resource= | =Suggest a tool or resource= | ||
Revision as of 13:16, 15 July 2015
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 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 - 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 - 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, Harvard Medical School, Boston, MA, USA - CRISPR Genome Engineering Resources:
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 - 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, Harvard Medical School, Boston, MA, USA - 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 - 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
- List of Drosophila reference genome assemblies at FlyBase, NCBI and UCSC. File:Drosophila Genome Assemblies.xls (spreadsheet) Updated June 17, 2015
- 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, 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 - 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 - FlyAnnotator, 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 - 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 - 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
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 - 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 - 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
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
- 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, Harvard Medical School, 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 - 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 - 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 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
- 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
Public Education
- droso4schools, An online resource for school lessons using the fruit fly Drosophila:
Manchester Fly Facility, University of Manchester, UK - 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 - 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 in cultured Drosophila cells:
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
- 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, 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
Suggest a tool or resource
- Please contact Flybase to suggest a tool or resource for the list.