Difference between revisions of "FlyBase:Drosophila Online Resources"

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=Atlases, Images and Videos=
 
=Atlases, Images and Videos=
* <b>Atlas of Drosophila Development</b>, An Atlas following the main events of embryogenesis and post-embryonic development:<br />[http://www.sdbonline.org/sites/fly/atlas/00atlas.htm Volker Hartenstein and Interactive Fly, Bethesda, MD, USA]
+
* <b>Atlas of Drosophila Development</b>, An Atlas following the main events of embryogenesis and post-embryonic development:<br />[https://www.sdbonline.org/sites/fly/atlas/00atlas.htm Volker Hartenstein and Interactive Fly, Bethesda, MD, USA]
* <b>BDTNP</b>, A cellular resolution 3D gene expression and morphology Atlas of the blastoderm:<br />[http://bdtnp.lbl.gov/Fly-Net/bioimaging.jsp?w=summary Berkeley Drosophila Transcription Network Project, University of California, Berkeley, USA]
+
* <b>FlyBase Maps</b>, A collection of illustrated and electron micrograph maps of polytene chromosomes for the 12 originally sequenced Drosophila species:<br />[http://flybase.org/wiki/FlyBase:Maps FlyBase Maps]
* <b>BrainTrap</b>, a collection of 3D confocal datasets taken from EYFP expressing protein trap Drosophila lines from the Cambridge Protein Trap project: <br />[http://fruitfly.inf.ed.ac.uk/braintrap/ Armstrong Lab, University of Edinburgh, Edinburgh, UK]
 
* <b>CSIRO</b> Anatomical Atlas of Flies:<br />[http://www.ento.csiro.au/biology/fly/fly.html# CSIRO Entomology, Australia]
 
* <b>Electron micrograph maps</b> of ''D. melanogaster'' polytene chromosomes:<br />[http://www.helsinki.fi/~saura/EM/index.html Sorsa Maps, Helsinki, Finland]
 
* <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]
 
* <b>FlyCircuit</b>, a Database of Drosophila Brain Neurons:<br />[http://www.flycircuit.tw/ FlyCircuit, National Tsing Hua University, Taiwan]
 
* <b>FlyGut</b>, An interactive Database that aims to provide a comprehensive atlas of the Drosophila melanogaster adult midgut (see also, [http://flygutseq.buchonlab.com/ FlyGut-seq]):<br />[http://flygut.epfl.ch/ Buchon Lab, Cornell University, Ithaca, NY, USA & Lemaitre Lab, EPFL, Lausanne, Switzerland]
 
 
* <b>FlyMove</b>, 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]
 
* <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]
 
* <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]
 
* <b>FlyView</b>, 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]
 
* <b>GETDB</b>, 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]
* <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]
+
* <b>Jove</b>, videos of experimental techniques:<br />[https://www.jove.com/search? 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]
+
* <b>MidgutAtlas</b>, Gene expression in five pH-defined regions of the larval midgut of D. melanogaster:<br />[https://flyatlas.gla.ac.uk/MidgutAtlas/index.html Dow laboratory, University of Glascow, Scotland, UK]
* <b>Learning to Fly</b>, a poster describing marker phenotypes in the fruit fly:<br />[http://onlinelibrary.wiley.com/journal/10.1002/%28ISSN%291526-968X/homepage/free_posters.htm Genesis (Journal), Wiley Online Library]
+
* <b>PeptideAtlas</b>, a multi-organism, publicly accessible compendium of peptides identified in a large set of tandem mass spectrometry proteomics experiments: <br />[https://peptideatlas.org/ Seattle Proteome Center, Seattle, Washington, USA]
* <b>PeptideAtlas</b>, a multi-organism, publicly accessible compendium of peptides identified in a large set of tandem mass spectrometry proteomics experiments: <br />[http://www.peptideatlas.org/ Seattle Proteome Center, Seattle, Washington, 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]
 
 
* <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]
 
* <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]
 +
 +
=Cell Lines and Cell Culture=
 +
* <b>Cellosaurus</b>: A thesaurus of cell lines which attempts to list all cell lines used in biomedical research.<br /> [https://www.cellosaurus.org/ Swiss Institute of Bioinformatics, Geneva, Switzerland]
 +
* <b>DGRC: Cell Line Catalog</b>: <br /> [https://dgrc.bio.indiana.edu/ Drosophila Genomics Resource Center, Indiana University, Bloomington, IN, USA]
 +
* <b>DGRC: Cell Culture Protocols</b>: <br />[https://dgrc.bio.indiana.edu/Protocols?tab=cells Drosophila Genomics Resource Center, Indiana University,  Bloomington, IN, USA]
 +
* <b>DGRC: Cell Culture FAQ Page</b>: <br />[https://dgrc.bio.indiana.edu/FAQs?tab=cells Drosophila Genomics Resource Center, Indiana University, Bloomington, IN, USA]
 +
* <b>DGRC: Feeder Cells</b>: <br />[https://dgrc.bio.indiana.edu/cells/FeederCells Drosophila Genomics Resource Center, Indiana University, Bloomington, IN, USA]
 +
* <b>DGRC: Fly Extract</b>:<br />[https://dgrc.bio.indiana.edu/cells/FlyExtract Drosophila Genomics Resource Center, Indiana University, Bloomington, IN, USA]
 +
* <b>DRSC: General information about cell lines</b>: <br />[https://fgr.hms.harvard.edu/drosophila-cultured-cell-lines DRSC, Harvard Medical School, Boston, MA, USA]
 +
* <b>DSRC: Resource information about CRISPR modified cell lines</b>: <br />[https://fgr.hms.harvard.edu/crispr-modified-cell-lines DRSC, Harvard Medical School, Boston, MA, USA]
 +
* <b>DRSC: Protocol information about CRISPR modification of cell lines</b>: <br />[https://fgr.hms.harvard.edu/cell-based-crispr DRSC, Harvard Medical School, Boston, MA, USA]
  
 
=CRISPRs and TALENs=
 
=CRISPRs and TALENs=
* <b>Cas9 Design</b>:<br />[http://cas9.cbi.pku.edu.cn/ Center for Bioinformatics, Peking University, Peking, China]
+
* <b>Addgene sgRNA Libraries</b>: Pooled sgRNA libraries for pooled CRISPR cell screening <br />[https://www.addgene.org/search/catalog/pooled-libraries/?q=Drosophila Addgene, Watertown, MA, USA]
* <b>CCTop</b> CRISPR/Cas9 optimum target finder:<br />[http://crispr.cos.uni-heidelberg.de/ Center for Organismal Studies, Heidelberg University, Heidelberg, DE]
+
* <b>CCTop</b> CRISPR/Cas9 optimum target finder:<br />[https://cctop.cos.uni-heidelberg.de/index.html Center for Organismal Studies, Heidelberg University, Heidelberg, DE]
* <b>CHOPCHOP</b> CRISPR/Cas9 target online predictor, mammalian and other major model organisms including fly:<br />[https://chopchop.rc.fas.harvard.edu/about.php/ Schier Lab, Harvard University, Cambridge, MA, Church Lab, Harvard Medical School, Boston, MA, USA]
+
* <b>CHOPCHOP</b> CRISPR/Cas9 target online predictor, mammalian and other major model organisms including fly:<br />[https://chopchop.cbu.uib.no/ University of Bergen, Bergen, Norway]
* <b>CRISPOR</b> Model organism gRNA design tool:<br />[http://tefor.net/crispor/crispor.cgi/ TEFOR, Gif-sur-Yvette, France]
 
* <b>CRISPR/Cas Web Resources</b> Web Resources for design and planning of CRISPR/Cas9 studies:<br />[http://igtrcn.org/knowledgebase/crisprcas-web-resources// IGTRCN, Insect Genetic Technologies Research Coordination Network, University of Maryland, Rockville, MD, USA]
 
 
* <b>CRISPR-ERA</b> A Fast and Comprehensive Guide RNA Design Tool for Genome Editing, Repression and Activation:<br />[http://crispr-era.stanford.edu// Lei Stanley Qi Lab and Xiaowo Wang Lab, Stanford University, Palo Alto, CA, USA]
 
* <b>CRISPR-ERA</b> A Fast and Comprehensive Guide RNA Design Tool for Genome Editing, Repression and Activation:<br />[http://crispr-era.stanford.edu// Lei Stanley Qi Lab and Xiaowo Wang Lab, Stanford University, Palo Alto, CA, USA]
* <b>CRISPR Genome Engineering Resources</b> CRISPR Design Tool:<br />[http://www.genome-engineering.org/crispr/?page_id=41/  Zhang Lab, MIT, Boston, MA, USA]
+
* <b>CRISPR fly design</b> -- reagents, protocols, and results from fly CRISPR/Cas experiments:<br />[http://crisprflydesign.org/ Bullolk Lab, MRC Laboratory of Molecular Biology, Cambridge, UK]
* <b>CRISPR fly design</b> -- reagents, protocols, and results from fly CRISPR/Cas experiments:<br />[http://www.crisprflydesign.org/ Bullolk Lab, MRC Laboratory of Molecular Biology, Cambridge, UK]
+
* <b>CRISPResso2 </b> CRISPR Design Tool:<br />[http://crispresso.pinellolab.org/submission Broad Institute, Cambridge, MA, Harvard Medical School, Boston, MA, Massachusetts General Hospital, Boston, MA, Dana Farber Cancer Center, Boston, MA, Children's Hospital, Boston, MA]
 
* <b>CRISPRscan</b> Novel scoring algorithm for selecting sgRNAs<br />[http://www.crisprscan.org// Giraldez Lab, Yale University, New Haven, CT, USA]
 
* <b>CRISPRscan</b> Novel scoring algorithm for selecting sgRNAs<br />[http://www.crisprscan.org// Giraldez Lab, Yale University, New Haven, CT, USA]
* <b>DRSC CRISPR Efficiency Tool for Assessment of Designs</b>:<br />[http://www.flyrnai.org/evaluateCrispr/ DRSC/TRiP-FGR, Harvard Medical School, Boston, MA, USA]
+
* <b>DGRC Cell lines and vector reagents for CRISPR</b>:<br />[https://dgrc.bio.indiana.edu/Search?category=&query=crispr Drosophila Genomics Resource Center (DGRC), Indiana University, Bloomington, IN, USA]
* <b>DRSC Finding CRISPRs</b>, Drosophila CRISPR gRNA design search tool:<br />[http://www.flyrnai.org/crispr2/ DRSC/TRiP-FGR, Harvard Medical School, Boston, MA, USA]
+
* <b>DGRC sgRNA libraries</b>:<br />[https://dgrc.bio.indiana.edu/gRNA Drosophila Genomics Resource Center (DGRC), Indiana University, Bloomington, IN, USA]
 +
* <b>DRSC CRISPR Efficiency Tool for Assessment of Designs</b>:<br />[https://www.flyrnai.org/evaluateCrispr/ DRSC/TRiP-FGR, Harvard Medical School, Boston, MA, USA]
 +
* <b>DRSC Find CRISPRs</b>, Drosophila CRISPR gRNA design search tool:<br />[https://www.flyrnai.org/crispr2/ DRSC/TRiP-FGR, Harvard Medical School, Boston, MA, USA]
 +
* <b>TRiP CRISPR fly stock information</b>:<br />[https://fgr.hms.harvard.edu/crispr-fly-stocks-and-vectors DRSC/TRiP-FGR, Harvard Medical School, Boston, MA, USA]
 +
* <b>DRSC cell-based CRISPR modification</b>:<br />[https://fgr.hms.harvard.edu/publications/technology/fly-cell-based-crispr DRSC/TRiP-FGR, Harvard Medical School, Boston, MA, USA]
 
* <b>E-CRISP</b>, Design of CRISPR Constructs:<br />[http://www.e-crisp.org/E-CRISP/designcrispr.html DKFZ/Boutros lab, Heildelberg, Germany]
 
* <b>E-CRISP</b>, Design of CRISPR Constructs:<br />[http://www.e-crisp.org/E-CRISP/designcrispr.html DKFZ/Boutros lab, Heildelberg, Germany]
 
* <b>E-TALEN</b>, Design of TALEN Constructs:<br />[http://www.e-talen.org/E-TALEN/ DKFZ/Boutros lab, Heildelberg, Germany]
 
* <b>E-TALEN</b>, Design of TALEN Constructs:<br />[http://www.e-talen.org/E-TALEN/ DKFZ/Boutros lab, Heildelberg, Germany]
* <b>flyCRISPR</b>, Resource Site: <br />[http://flycrispr.molbio.wisc.edu/ O'Connor-Giles, Wildonger, and Harrison Labs, University of Wisconsin-Madison, WI, USA]
+
* <b>flyCRISPR</b>, Overview: <br />[https://flycrispr.org/ O'Connor-Giles, Wildonger, and Harrison Labs, University of Wisconsin-Madison, WI, USA]
* <b>flyCRISPR</b>, Optimal Target Finder:<br />[http://tools.flycrispr.molbio.wisc.edu/targetFinder/ O'Connor-Giles Lab, University of Wisconsin-Madison, WI, USA]
+
* <b>flyCRISPR</b>, Target Finder:<br />[https://flycrispr.org/target-finder/ O'Connor-Giles Lab, University of Wisconsin-Madison, WI, USA]
* <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]
+
* <b>Genome Engineering by CRISPR/Cas9 in Drosophila</b>:<br />[https://shigen.nig.ac.jp/fly/nigfly/cas9/ NIG/FLY/Ueda lab, Mishima, Japan]
 
* <b>Mojo Hand</b>, 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]
* <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]
 
* <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]
 
* <b>TAL Effectors</b>:<br />[http://taleffector.genome-engineering.org/ Zhang lab, MIT, Boston, MA, USA]
 
 
* <b>TALengineering.org</b>, 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]
* <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]
+
* <b>TRiP: Overview of sgRNA vectors</b>:<br />[https://fgr.hms.harvard.edu/sgrna-vectors TRiP, Harvard Medical School, Boston, MA, USA]
 +
* <b>Zhang Lab CRISPR Plasmids Available from Addgene</b> CRISPR Plasmids:<br />[https://www.addgene.org/crispr/zhang/ Zhang Lab, MIT, Boston, MA, USA]
  
 
=Data Repositories=
 
=Data Repositories=
* <b>Array Express</b> - Functional Genomics Data:<br />[http://www.ebi.ac.uk/arrayexpress/ Array Express, EMBL-EBI, Hinxton, UK]
+
* <b>Array Express</b> - Functional Genomics Data:<br />[https://www.ebi.ac.uk/arrayexpress/ Array Express, EMBL-EBI, Hinxton, UK]
* <b>Berkeley Drosophila Genome Project (BDGP)</b>:<br />[http://www.fruitfly.org/ BDGP, University of California, Berkeley, USA]
+
* <b>Berkeley Drosophila Genome Project (BDGP)</b>:<br />[https://www.fruitfly.org/ BDGP, University of California, Berkeley, USA]
* <b>DDBJ</b>, 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 />[https://www.ddbj.nig.ac.jp/index-e.html DDBJ, National Institute of Genetics, Mishima, Japan]
* <b>EMBL-EBI</b>, The European Bioinformatics Institute:<br />[http://www.ebi.ac.uk/ EMBL-EBI, Hinxton, UK]
+
* <b>EMBL-EBI</b>, The European Bioinformatics Institute:<br />[https://www.ebi.ac.uk/ 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]
+
* <b>ENA</b>, European Nucleotide Archive:<br />[https://www.ebi.ac.uk/ena/browser/home ENA, European Nucleotide Archive, EMBL-EBI, Hinxton, UK]
* <b>Ensembl Genome Browser</b>:<br />[http://useast.ensembl.org/index.html EMBL-EBI, Hinxton, UK]
+
* <b>ENCODE</b>, Encyclopedia of DNA Elements (including modENCODE and modERN):<br />[https://www.encodeproject.org/ ENCODE, Stanford University, Stanford, USA]
* <b>Gene Disruption Project (GDP)</b>:<br />[http://flypush.imgen.bcm.tmc.edu/pscreen/ GDP, Baylor College of Medicine, Texas]<br />[http://flypush.imgen.bcm.tmc.edu/pscreen/transposons.html Schematic drawings of Transposons]
+
* <b>Gene Disruption Project (GDP)</b>:<br />[https://flypush.research.bcm.edu/pscreen/index.php GDP, Baylor College of Medicine, Texas]<br />[https://flypush.research.bcm.edu/pscreen/transposons.html Schematic drawings of Transposons]
* <b>GenBank</b>,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 />[https://www.ncbi.nlm.nih.gov/genbank/ GenBank, NCBI, Bethesda, USA]
* <b>GEO Datasets</b>, 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 />[https://www.ncbi.nlm.nih.gov/geo/info/datasets.html NCBI, Bethesda, USA]
* <b>NCBI</b>, National Center fo Biotechnology Information:<br />[http://www.ncbi.nlm.nih.gov Bethesda, MD USA]
+
* <b>modERN</b>, model organism Encyclopedia of Regulatory Networks:<br />[http://epic.gs.washington.edu/modERN/ modERN, University of Washington, Seattle, USA]
* <b>NCBI Map Viewer</b>, A genome view of Drosophila melanogaster:<br />[http://www.ncbi.nlm.nih.gov/mapview/map_search.cgi?taxid=7227 NCBI, Bethesda, MD USA]
+
* <b>NCBI</b>, National Center for Biotechnology Information:<br />[http://www.ncbi.nlm.nih.gov Bethesda, MD USA]
* <b>PubMed</b>, Biomedical literature full-text archive:<br />[http://www.ncbi.nlm.nih.gov/pubmed PubMed, NCBI, Bethesda, MD USA]
+
* <b>NCBI Genome Data Viewer</b>, A genome view of Drosophila melanogaster:<br />[https://www.ncbi.nlm.nih.gov/genome/gdv/?org=drosophila-melanogaster NCBI, Bethesda, USA]
* <b>PubMed Central</b>, Biomedical literature citations and abstracts:<br />[http://www.ncbi.nlm.nih.gov/pmc/ PubMed Central, NCBI, Bethesda, MD USA]
+
* <b>PubMed</b>, Biomedical literature full-text archive:<br />[https://pubmed.ncbi.nlm.nih.gov/ PubMed, NCBI, Bethesda, USA]
* <b>SRA</b>, Sequence Read Archive:<br />[http://www.ncbi.nlm.nih.gov/sra SRA, NCBI, Bethesda, MD, USA]
+
* <b>PubMed Central</b>, Biomedical literature citations and abstracts:<br />[https://www.ncbi.nlm.nih.gov/pmc/ PubMed Central, NCBI, Bethesda, USA]
* <b>UCSC Genome Browser Gateway</b> - D. melanogaster:<br />[http://genome.ucsc.edu/cgi-bin/hgGateway UCSC Genome Browser, UC Santa Cruz, USA]
+
* <b>SRA</b>, Sequence Read Archive:<br />[https://www.ncbi.nlm.nih.gov/sra SRA, NCBI, Bethesda, MD, USA]
 +
* <b>UCSC Genome Browser Gateway</b> - D. melanogaster:<br />[http://genome.ucsc.edu/cgi-bin/hgGateway UCSC Genome Browser, UC Santa Cruz, Santa Cruz, USA]
 +
 
 +
=DNA Reagents=
 +
* <b>Addgene Highly requested Drosophila plasmids</b>: <br />[https://www.addgene.org/search/catalog/pooled-libraries/?q=Drosophila Addgene, Watertown, MA, USA]
 +
* <b>Addgene sgRNA Libraries</b>: Pooled sgRNA libraries for pooled CRISPR cell screening <br />[https://www.addgene.org/search/catalog/pooled-libraries/?q=Drosophila Addgene, Watertown, MA, USA]
 +
* <b>DNASU Drosophila plasmids</b>: <br />[https://dnasu.org/DNASU/AdvancedSearchOptions.do?species=Drosophila%20melanogaster&psi=0 DNASU Plasmid Repository, Arizona State University, Tempe, AZ, USA]
 +
* <b>DGRC DNA Clones Catalog</b>:<br />[https://dgrc.bio.indiana.edu/clones/Catalog Drosophila Genomics Resource Center, Indiana University, Bloomington, IN, USA]
 +
* <b>DGRC DNA Clone Collections</b>:<br />[https://dgrc.bio.indiana.edu/clones/BulkCollections  Drosophila Genomics Resource Center, Indiana University, Bloomington, IN, USA]
 +
* <b>DGRC DNA Clone FAQ Page</b>:<br />[https://dgrc.bio.indiana.edu/FAQs?tab=clones Drosophila Genomics Resource Center, Indiana University, Bloomington, IN, USA]
 +
* <b>DGRC DNA Clone Protocols</b>:<br />[https://dgrc.bio.indiana.edu/Protocols?tab=clones Drosophila Genomics Resource Center, Indiana University, Bloomington, IN, USA]
 +
* <b>DGRC DNA Vectors Catalog</b>:<br />[https://dgrc.bio.indiana.edu/vectors/Catalog Drosophila Genomics Resource Center, Indiana University, Bloomington, IN, USA]
 +
* <b>DGRC DNA Vectors FAQs Page</b>:<br />[https://dgrc.bio.indiana.edu/FAQs?tab=vectors Drosophila Genomics Resource Center, Indiana University, Bloomington, IN, USA]
 +
* <b>DGRC DNA Vectors Protocols</b>:<br />[https://dgrc.bio.indiana.edu/Protocols?tab=vectors Drosophila Genomics Resource Center, Indiana University, Bloomington, IN, USA]
 +
* <b>TRiP: VALIUM and WALIUM plasmid vector sets</b>:<br />[https://fgr.hms.harvard.edu/trip-plasmid-vector-sets TRiP, Harvard Medical School, Boston, MA, USA]
 +
* <b>TRiP: Plasmid cloning protocols</b>:<br />[https://fgr.hms.harvard.edu/cloning-and-sequencing TRiP, Harvard Medical School, Boston, MA, USA]
 +
* <b>TRiP: Overview of sgRNA vectors</b>:<br />[https://fgr.hms.harvard.edu/sgrna-vectors TRiP, Harvard Medical School, Boston, MA, USA]
  
=Data and Metadata for Drosophila Genomes=
+
=Drosophila Genomes Data and Metadata=
 +
* <b>DrosOmics</b>, a comparative genomics browser to explore omics data in 52 natural populations of D. melanogaster:<br />[https://www.biologiaevolutiva.org/gonzalez_lab/drosomics/ Institute of Evolutionary Biology, CSIC, Universitat Pompeu Fabra, Barcelona, Spain]
 
* <b>DroSpeGe</b>, a view of Drosophila genome data, with genome maps and BLAST sequence search, for 12 species:<br />[http://insects.eugenes.org/species/ Genome Informatics Lab, Indiana University, Bloomington, Indiana, USA]
 
* <b>DroSpeGe</b>, a view of Drosophila genome data, with genome maps and BLAST sequence search, for 12 species:<br />[http://insects.eugenes.org/species/ Genome Informatics Lab, Indiana University, Bloomington, Indiana, USA]
 
* <b>List of Drosophila reference genome assemblies</b> at FlyBase, NCBI and UCSC. [[File:DrosophilaGenomeAssemblies.xls]] (spreadsheet) ''Updated June 17, 2015''
 
* <b>List of Drosophila reference genome assemblies</b> at FlyBase, NCBI and UCSC. [[File:DrosophilaGenomeAssemblies.xls]] (spreadsheet) ''Updated June 17, 2015''
* <b>''D. albomicans'' Genome</b>:<br />[http://www.ncbi.nlm.nih.gov/genome/2712/ D. albomicans Organism Overview, NCBI, USA]<br />[http://www.ncbi.nlm.nih.gov/genome/genomes/2712/ D. albomicans Genome Assembly Report, 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 />[https://www.ncbi.nlm.nih.gov/genome/2712/ ''D. albomicans'' Organism Overview, NCBI, USA]<br />[https://www.ncbi.nlm.nih.gov/genome/genomes/2712/ ''D. albomicans'' Genome Assembly Report, NCBI, USA]<br />[http://www.ebi.ac.uk/ena/data/view/GCA_000298335 ''D. albomicans'' 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.ncbi.nlm.nih.gov/genome/genomes/244/ D. ananassae Genome Assembly Report, NCBI, USA]<br />[http://www.ebi.ac.uk/ena/data/view/GCA_000005115 D. ananassae Genome Assembly Report, ENA, UK]
+
* <b>''D. americana'' Genome</b>:<br />[https://www.ncbi.nlm.nih.gov/genome/10917 ''D. americana'' Organism Overview, NCBI, USA]<br />[https://www.ncbi.nlm.nih.gov/genome/genomes/10917 ''D. americana'' Genome Assembly Report, NCBI, USA]<br />[http://www.ebi.ac.uk/ena/data/view/GCA_001245305.1 ''D. americana'' 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.ncbi.nlm.nih.gov/genome/genomes/3499/ D. biarmipes Genome Assembly Report, NCBI, USA]<br />[http://www.ebi.ac.uk/ena/data/view/GCA_000233415 D. biarmipes Genome Assembly Report, ENA, UK]
+
* <b>''D. ananassae'' Genome</b>:<br />[https://www.ncbi.nlm.nih.gov/genome/244/ ''D. ananassae'' Organism Overview, NCBI, USA]<br />[https://www.ncbi.nlm.nih.gov/genome/genomes/244/ ''D. ananassae'' Genome Assembly Report, NCBI, USA]<br />[http://www.ebi.ac.uk/ena/data/view/GCA_000005115 ''D. ananassae'' 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.ncbi.nlm.nih.gov/genome/genomes/3489/ D. bipectinata Genome Assembly Report, NCBI, USA]<br />[http://www.ebi.ac.uk/ena/data/view/GCA_000236285 D. bipectinata Genome Assembly Report, ENA, UK]
+
* <b>''D. arizonae'' Genome</b>:<br />[https://www.ncbi.nlm.nih.gov/genome/45090/ ''D. arizonae'' Organism Overview, NCBI, USA]<br />[https://www.ncbi.nlm.nih.gov/genome/genomes/45090/ ''D. arizonae'' Genome Assembly and Annotation Report, NCBI, USA]<br />[https://www.ebi.ac.uk/ena/data/view/GCA_001654025 ''D. arizonae'' Genome Assembly Report, ENA, UK]
* <b>''D. erecta'' Genome</b>:<br />[http://www.ncbi.nlm.nih.gov/genome/250/ D. erecta Organism Overview, NCBI, USA]<br />[http://www.ncbi.nlm.nih.gov/genome/genomes/250/ D. erecta Genome Assembly Report, NCBI, USA]<br />[http://www.ebi.ac.uk/ena/data/view/GCA_000005135 D. erecta Genome Assembly Report, ENA, UK]
+
* <b>''D. biarmipes'' Genome</b>:<br />[https://www.ncbi.nlm.nih.gov/genome/3499/ ''D. biarmipes'' Organism Overview, NCBI, USA]<br />[https://www.ncbi.nlm.nih.gov/genome/genomes/3499/ ''D. biarmipes'' Genome Assembly Report, NCBI, USA]<br />[http://www.ebi.ac.uk/ena/data/view/GCA_000233415 ''D. biarmipes'' 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.ncbi.nlm.nih.gov/genome/genomes/3490 D. elegans Genome Assembly Report, NCBI, USA]<br />[http://www.ebi.ac.uk/ena/data/view/GCA_000224195 D. elegans Genome Assembly Report, ENA, UK]
+
* <b>''D. bipectinata'' Genome</b>:<br />[https://www.ncbi.nlm.nih.gov/genome/3489/ ''D. bipectinata'' Organism Overview, NCBI, USA]<br />[https://www.ncbi.nlm.nih.gov/genome/genomes/3489/ ''D. bipectinata'' Genome Assembly Report, NCBI, USA]<br />[http://www.ebi.ac.uk/ena/data/view/GCA_000236285 ''D. bipectinata'' 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.ncbi.nlm.nih.gov/genome/genomes/6863/ D. eugracilis Genome Assembly Report, NCBI, USA]<br />[http://www.ebi.ac.uk/ena/data/view/GCA_000236325 D. eugracilis Genome Assembly Report, ENA, UK]
+
* <b>''D. busckii'' Genome</b>:<br />[https://www.ncbi.nlm.nih.gov/genome/38276/ ''D. busckii'' Organism Overview, NCBI, USA]<br />[https://www.ncbi.nlm.nih.gov/genome/genomes/38276/ ''D. busckii'' Genome Assembly Report, NCBI, USA]<br />[http://www.ebi.ac.uk/ena/data/view/GCA_001277935 ''D. busckii'' 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.ncbi.nlm.nih.gov/genome/genomes/3491/ D. ficusphila Genome Assembly Report, NCBI, USA]<br />[http://www.ebi.ac.uk/ena/data/view/GCA_000220665 D. ficusphila Genome Assembly Report, ENA, UK]
+
* <b>''D. erecta'' Genome</b>:<br />[https://www.ncbi.nlm.nih.gov/genome/250/ ''D. erecta'' Organism Overview, NCBI, USA]<br />[https://www.ncbi.nlm.nih.gov/genome/genomes/250/ ''D. erecta'' Genome Assembly Report, NCBI, USA]<br />[http://www.ebi.ac.uk/ena/data/view/GCA_000005135 ''D. erecta'' 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.ncbi.nlm.nih.gov/genome/genomes/257/ D. grimshawi Genome Assembly Report, NCBI, USA]<br />[http://www.ebi.ac.uk/ena/data/view/GCA_000005155 D. grimshawi Genome Assembly Report, ENA, UK]
+
* <b>''D. elegans'' Genome</b>:<br />[https://www.ncbi.nlm.nih.gov/genome/3490 ''D. elegans'' Organism Overview, NCBI, USA]<br />[https://www.ncbi.nlm.nih.gov/genome/genomes/3490 ''D. elegans'' Genome Assembly Report, NCBI, USA]<br />[http://www.ebi.ac.uk/ena/data/view/GCA_000224195 ''D. elegans'' Genome Assembly Report, ENA, UK]
* <b>''D. kikkawai'' Genome</b>:<br />[http://www.ncbi.nlm.nih.gov/genome/3492/ D. kikkawai Organism Overview, NCBI, USA]<br />[http://www.ncbi.nlm.nih.gov/genome/genomes/3492/ D. kikkawai Genome Assembly Report, NCBI, USA]<br />[http://www.ebi.ac.uk/ena/data/view/GCA_000224215 D. kikkawai Genome Assembly Report, ENA, UK]
+
* <b>''D. eugracilis'' Genome</b>:<br />[https://www.ncbi.nlm.nih.gov/genome/6863/ ''D. eugracilis'' Organism Overview, NCBI, USA]<br />[https://www.ncbi.nlm.nih.gov/genome/genomes/6863/ ''D. eugracilis'' Genome Assembly Report, NCBI, USA]<br />[http://www.ebi.ac.uk/ena/data/view/GCA_000236325 ''D. eugracilis'' 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.ncbi.nlm.nih.gov/genome/genomes/47/ D. melanogaster Genome Assembly Report, NCBI, USA]<br />[http://www.ebi.ac.uk/ena/data/view/GCA_000001215 D. melanogaster Genome Assembly Report, ENA, UK]
+
* <b>''D. ficusphila'' Genome</b>:<br />[https://www.ncbi.nlm.nih.gov/genome/3491/ ''D. ficusphila'' Organism Overview, NCBI, USA]<br />[https://www.ncbi.nlm.nih.gov/genome/genomes/3491/ ''D. ficusphila'' Genome Assembly Report, NCBI, USA]<br />[http://www.ebi.ac.uk/ena/data/view/GCA_000220665 ''D. ficusphila'' 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.ncbi.nlm.nih.gov/genome/genomes/10915/ D. miranda Genome Assembly Report, NCBI, USA]<br />[http://www.ebi.ac.uk/ena/data/view/GCA_000269505 D. miranda Genome Assembly Report, ENA, UK]
+
* <b>''D. grimshawi'' Genome</b>:<br />[https://www.ncbi.nlm.nih.gov/genome/257/ ''D. grimshawi'' Organism Overview, NCBI, USA]<br />[https://www.ncbi.nlm.nih.gov/genome/genomes/257/ ''D. grimshawi'' Genome Assembly Report, NCBI, USA]<br />[http://www.ebi.ac.uk/ena/data/view/GCA_000005155 ''D. grimshawi'' 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.ncbi.nlm.nih.gov/genome/genomes/259/ D. mojavensis Genome Assembly Report, NCBI, USA]<br />[http://www.ebi.ac.uk/ena/data/view/GCA_000005175 D. mojavensis Genome Assembly Report, ENA, UK]
+
* <b>''D. kikkawai'' Genome</b>:<br />[https://www.ncbi.nlm.nih.gov/genome/3492/ ''D. kikkawai'' Organism Overview, NCBI, USA]<br />[https://www.ncbi.nlm.nih.gov/genome/genomes/3492/ ''D. kikkawai'' Genome Assembly Report, NCBI, USA]<br />[http://www.ebi.ac.uk/ena/data/view/GCA_000224215 ''D. kikkawai'' 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.ncbi.nlm.nih.gov/genome/genomes/265/ D. persimilis Genome Assembly Report, NCBI, USA]<br />[http://www.ebi.ac.uk/ena/data/view/GCA_000005195 D. persimilis Genome Assembly Report, ENA, UK]
+
* <b>''D. melanogaster'' Genome</b>:<br />[https://www.ncbi.nlm.nih.gov/genome/47/ ''D. melanogaster'' Organism Overview, NCBI, USA]<br />[https://www.ncbi.nlm.nih.gov/genome/genomes/47/ ''D. melanogaster'' Genome Assembly Report, NCBI, USA]<br />[http://www.ebi.ac.uk/ena/data/view/GCA_000001215 ''D. melanogaster'' Genome Assembly Report, ENA, UK]
* <b>''D. pseudoobscura'' Genome</b>:<br />[http://www.ncbi.nlm.nih.gov/genome/219/ D. pseudoobscura Organism Overview, NCBI, USA]<br />[http://www.ncbi.nlm.nih.gov/genome/genomes/219/ D. pseudoobscura Genome Assembly Report, NCBI, USA]<br />[http://www.ebi.ac.uk/ena/data/view/GCA_000001765 D. pseudoobscura Genome Assembly Report, ENA, UK]
+
* <b>''D. miranda'' Genome</b>:<br />[https://www.ncbi.nlm.nih.gov/genome/10915/ ''D. miranda'' Organism Overview, NCBI, USA]<br />[https://www.ncbi.nlm.nih.gov/genome/genomes/10915/ ''D. miranda'' Genome Assembly Report, NCBI, USA]<br />[http://www.ebi.ac.uk/ena/data/view/GCA_000269505 ''D. miranda'' 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.ncbi.nlm.nih.gov/genome/genomes/6853/ D. rhopaloa Genome Assembly Report, NCBI, USA]<br />[http://www.ebi.ac.uk/ena/data/view/GCA_000236305 D. rhopaloa Genome Assembly Report, ENA, UK]
+
* <b>''D. mojavensis'' Genome</b>:<br />[https://www.ncbi.nlm.nih.gov/genome/259/ ''D. mojavensis'' Organism Overview, NCBI, USA]<br />[https://www.ncbi.nlm.nih.gov/genome/genomes/259/ ''D. mojavensis'' Genome Assembly Report, NCBI, USA]<br />[http://www.ebi.ac.uk/ena/data/view/GCA_000005175 ''D. mojavensis'' 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.ncbi.nlm.nih.gov/genome/genomes/271/ D. sechellia Genome Assembly Report, NCBI, USA]<br />[http://www.ebi.ac.uk/ena/data/view/GCA_000005215 D. sechellia Genome Assembly Report, ENA, UK]
+
* <b>''D. navojoa'' Genome</b>:<br />[https://www.ncbi.nlm.nih.gov/genome/45091/ ''D. navojoa'' Organism Overview, NCBI, USA]<br />[https://www.ncbi.nlm.nih.gov/genome/genomes/45091/ ''D. navojoa'' Genome Assembly Report, NCBI, USA]<br />[http://www.ebi.ac.uk/ena/data/view/GCA_001654015 ''D. navojoa'' 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.ncbi.nlm.nih.gov/genome/genomes/200/ D. simulans Genome Assembly Report, NCBI, USA]<br />[http://www.ebi.ac.uk/ena/data/view/GCA_000259045 D. simulans Genome Assembly Report, ENA, UK]
+
* <b>''D. persimilis'' Genome</b>:<br />[https://www.ncbi.nlm.nih.gov/genome/265/ ''D. persimilis'' Organism Overview, NCBI, USA]<br />[https://www.ncbi.nlm.nih.gov/genome/genomes/265/ ''D. persimilis'' Genome Assembly Report, NCBI, USA]<br />[http://www.ebi.ac.uk/ena/data/view/GCA_000005195 ''D. persimilis'' 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.ncbi.nlm.nih.gov/genome/genomes/18317/ D. suzukii Genome Assembly Report, NCBI, USA]<br />[http://www.ebi.ac.uk/ena/data/view/GCA_000472105 D. suzukii Genome Assembly Report, ENA, UK]
+
* <b>''D. pseudoobscura'' Genome</b>:<br />[https://www.ncbi.nlm.nih.gov/genome/219/ ''D. pseudoobscura'' Organism Overview, NCBI, USA]<br />[https://www.ncbi.nlm.nih.gov/genome/genomes/219/ ''D. pseudoobscura'' Genome Assembly Report, NCBI, USA]<br />[http://www.ebi.ac.uk/ena/data/view/GCA_000001765 ''D. pseudoobscura'' 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.ncbi.nlm.nih.gov/genome/genomes/3493/ D. takahashii Genome Assembly Report, NCBI, USA]<br />[http://www.ebi.ac.uk/ena/data/view/GCA_000224235 D. takahashii Genome Assembly Report, ENA, UK]
+
* <b>''D. rhopaloa'' Genome</b>:<br />[https://www.ncbi.nlm.nih.gov/genome/6853/ ''D. rhopaloa'' Organism Overview, NCBI, USA]<br />[https://www.ncbi.nlm.nih.gov/genome/genomes/6853/ ''D. rhopaloa'' Genome Assembly Report, NCBI, USA]<br />[http://www.ebi.ac.uk/ena/data/view/GCA_000236305 ''D. rhopaloa'' 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.ncbi.nlm.nih.gov/genome/genomes/261/ D. virilis Genome Assembly Report, NCBI, USA]<br />[http://www.ebi.ac.uk/ena/data/view/GCA_000005245 D. virilis Genome Assembly Report, ENA, UK]
+
* <b>''D. sechellia'' Genome</b>:<br />[https://www.ncbi.nlm.nih.gov/genome/271/ ''D. sechellia'' Organism Overview, NCBI, USA]<br />[https://www.ncbi.nlm.nih.gov/genome/genomes/271/ ''D. sechellia'' Genome Assembly Report, NCBI, USA]<br />[http://www.ebi.ac.uk/ena/data/view/GCA_000005215 ''D. sechellia'' 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.ncbi.nlm.nih.gov/genome/genomes/251/ D. willistoni Genome Assembly Report, NCBI, USA]<br />[http://www.ebi.ac.uk/ena/data/view/GCA_000005925 D. willistoni Genome Assembly Report, ENA, UK]
+
* <b>''D. simulans'' Genome</b>:<br />[https://www.ncbi.nlm.nih.gov/genome/200/ ''D. simulans'' Organism Overview, NCBI, USA]<br />[https://www.ncbi.nlm.nih.gov/genome/genomes/200/ ''D. simulans'' Genome Assembly Report, NCBI, USA]<br />[http://www.ebi.ac.uk/ena/data/view/GCA_000259045 ''D. simulans'' 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.ncbi.nlm.nih.gov/genome/genomes/148/ D. yakuba Genome Assembly Report, NCBI, USA]<br />[http://www.ebi.ac.uk/ena/data/view/GCA_000005975 D. yakuba Genome Assembly Report, ENA, UK]]
+
* <b>''D. suzukii'' Genome</b>:<br />[https://www.ncbi.nlm.nih.gov/genome/18317/ ''D. suzukii'' Organism Overview, NCBI, USA]<br />[https://www.ncbi.nlm.nih.gov/genome/genomes/18317/ ''D. suzukii'' Genome Assembly Report, NCBI, USA]<br />[http://www.ebi.ac.uk/ena/data/view/GCA_000472105 ''D. suzukii'' Genome Assembly Report, ENA, UK]<br /> [http://spottedwingflybase.org/ ''D. suzukii'' SpottedWingFlyBase The Spotted Wing Drosophila Project, UC Davis and Oregon State University, USA]
 +
* <b>''D. takahashii'' Genome</b>:<br />[https://www.ncbi.nlm.nih.gov/genome/3493/ ''D. takahashii'' Organism Overview, NCBI, USA]<br />[https://www.ncbi.nlm.nih.gov/genome/genomes/3493/ ''D. takahashii'' Genome Assembly Report, NCBI, USA]<br />[http://www.ebi.ac.uk/ena/data/view/GCA_000224235 ''D. takahashii'' Genome Assembly Report, ENA, UK]
 +
* <b>''D. virilis'' Genome</b>:<br />[https://www.ncbi.nlm.nih.gov/genome/261/ ''D. virilis'' Organism Overview, NCBI, USA]<br />[https://www.ncbi.nlm.nih.gov/genome/genomes/261/ ''D. virilis'' Genome Assembly Report, NCBI, USA]<br />[http://www.ebi.ac.uk/ena/data/view/GCA_000005245 ''D. virilis'' Genome Assembly Report, ENA, UK]
 +
* <b>''D. willistoni'' Genome</b>:<br />[https://www.ncbi.nlm.nih.gov/genome/251/ ''D. willistoni'' Organism Overview, NCBI, USA]<br />[https://www.ncbi.nlm.nih.gov/genome/genomes/251/ ''D. willistoni'' Genome Assembly Report, NCBI, USA]<br />[http://www.ebi.ac.uk/ena/data/view/GCA_000005925 ''D. willistoni'' Genome Assembly Report, ENA, UK]
 +
* <b>''D. yakuba'' Genome</b>:<br />[https://www.ncbi.nlm.nih.gov/genome/148/ ''D. yakuba'' Organism Overview, NCBI, USA]<br />[https://www.ncbi.nlm.nih.gov/genome/genomes/148/ ''D. yakuba'' Genome Assembly Report, NCBI, USA]<br />[http://www.ebi.ac.uk/ena/data/view/GCA_000005975 ''D. yakuba'' Genome Assembly Report, ENA, UK]]
  
 
=Gene Expression Databases and Tools=
 
=Gene Expression Databases and Tools=
* <b>BDGP in situ</b>, Patterns of gene expression in Drosophila embryogenesis:<br />[http://insitu.fruitfly.org/cgi-bin/ex/insitu.pl Gene expression database, BDGP, University of California, Berkeley, USA]
+
* <b>BDGP in situ</b>, Patterns of gene expression in Drosophila embryogenesis:<br />[https://insitu.fruitfly.org/cgi-bin/ex/insitu.pl Gene expression database, BDGP, University of California, Berkeley, USA]
* <b>BDTNP</b>, A cellular resolution 3D gene expression and morphology Atlas of the blastoderm.<br />[http://bdtnp.lbl.gov/Fly-Net/bioimaging.jsp?w=summary Berkeley Drosophila Transcription Network Project, University of California, Berkeley, USA]
+
* <b>BGee</b> Normal Gene Expression Data in Animals (based on RNA-Seq, Affymetrix, in situ hybridization, and EST data).<br />[https://www.bgee.org/ SIB, Swiss Institute of Bioinformatics, University of Lausanne, Lausanne, Switzerland]
* <b>BGee</b> Normal Gene Expression Data in Animals (based on RNA-Seq, Affymetrix, in situ hybridization, and EST data).<br />[http://bgee.org/ SIB, Swiss Institute of Bioinformatics, University of Lausanne, Lausanne, Switzerland]
+
* <b>DIGITtally</b>, Finding Genes of Interest DIGITtally: <br /> [https://www.digittally.org/ DIGITtally, University of Glasgow, Glasgow, UK]
* <b><em>cis</em>Patterns</b>, A database of over 100 Drosophila GAL4-driver lines regulated by single cis-regulatory enhancers:<br />[http://cispatterns.ninds.nih.gov/ Jermaine Ross and the Odenwald Lab, NINDS, NIH, Bethesda MD, USA]
+
* <b>FlyAtlas2</b>, for exploring how genes are expressed in the tissues of ''D. melanogaster'':<br />[https://flyatlas.gla.ac.uk/FlyAtlas2/index.html FlyAtlas2, University of Glasgow, Glasgow, UK]
* <b>Flannotator</b>, Annotation of Gene Expression:<br />[http://www.flyprot.org/index.php FlyAnnotator, University of Cambridge, 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]
 
* <b>FlyEx</b>, a Database of Segmentation Gene Expression in Drosophila:<br />[http://urchin.spbcas.ru/flyex/ FlyEx, St. Petersburg State Polytechnical University, Russia]
 
 
* <b>FlyExpress</b>, 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]
* <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]
+
* <b>Fly-FISH</b>, A Database of Drosophila Embryo mRNA Localizaton Patterns:<br />[https://fly-fish.ccbr.utoronto.ca/ Fly-FISH, University of Toronto, Toronto, Canada]
 
* <b>FlyGut-seq</b>, a transcriptomic resource that complements the original [http://flygut.epfl.ch/ Flygut website]:<br />[http://flygutseq.buchonlab.com/ Buchon Lab, Cornell University, Ithaca, NY, USA]
 
* <b>FlyGut-seq</b>, a transcriptomic resource that complements the original [http://flygut.epfl.ch/ Flygut website]:<br />[http://flygutseq.buchonlab.com/ Buchon Lab, Cornell University, Ithaca, NY, USA]
* <b>FlyLight</b>, Expression Patterns of GAL4 Driver Lines:<br />[http://flweb.janelia.org/cgi-bin/flew.cgi HHMI, Janelia Farms Research Campus]
+
* <b>FlyLight</b>, Expression Patterns of GAL4, LexA, and Split-GAL4 Driver Lines to enable the visualization and precise manipulation of individual cell types in the Drosophila nervous system:<br />[https://www.janelia.org/project-team/flylight HHMI, Janelia Farms Research Campus]
* <b>FlyOde</b>, FLY Organ Developmental Network: <br /> [http://flyode.boun.edu.tr/index.html FlyOde, Bogazici University, Istanbul, Turkey]
+
* <b>flytrap</b>, a database of P{GAL4} enhancer traps and their expression in brains: <br />[https://www.fly-trap.org/ flytrap, University of Edinburgh, UK]
* <b>flytrap</b>, a database of P{GAL4} enhancer traps and their expression in brains: <br />[http://www.fly-trap.org/ flytrap, University of Edinburgh, UK]
+
* <b>Gene Expression Levels by Cell Line</b> (based on modENCODE data):<br />[https://www.flyrnai.org/cgi-bin/RNAi_expression_levels.pl DRSC/TRiP-FGR, Harvard Medical School, Boston, MA, USA]
* <b>Gene Expression Levels by Cell Line</b> (based on modENCODE data):<br />[http://www.flyrnai.org/cgi-bin/RNAi_expression_levels.pl DRSC/TRiP-FGR, Harvard Medical School, Boston, MA, USA]
+
* <b>GEO Profiles</b>, Gene Expression Omnibus:<br />[https://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]
+
* <b>MidgutAtlas</b>, Gene expression in five pH-defined regions of the larval midgut of D. melanogaster:<br />[http://flyatlas.gla.ac.uk/MidgutAtlas/index.html Dow laboratory, University of Glascow, Scotland, UK]
* <b>modENCODE Tiling Path Expression Search</b> (based on modENCODE data):<br />[https://dgrc.cgb.indiana.edu/cells/TilingSearch DGRC, University of Indiana, Bloomington, IN, USA]
+
* <b>RNAMiner</b>, A Bioinformatics Protocol for Mining Large RNA-Seq Transcriptomics Data:<br />[https://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=
* <b>FlyBase Gene Groups</b>, Manually curated reports on functionally related genes, based on the literature:<br /> [http://flybase.org/static_pages/FBgg/browse.html Gene group list, FlyBase]
+
* <b>FlyBase Gene Groups</b>, Manually curated reports on functionally related genes, based on the literature:<br /> [https://flybase.org/lists/FBgg/ Gene group list, FlyBase]
* <b>GLAD</b>, an Online Database of Gene List Annotations for Drosophila:<br /> [http://www.flyrnai.org/tools/glad/web/ DRSC/TRiP-FGR, Harvard Medical School, Boston, MA, USA]
+
* <b>FlyBase Signaling Pathways</b>, Manually curated reports on Signaling Pathways, based on the literature:<br /> [https://flybase.org/lists/FBgg/pathways Pathways list, FlyBase]
* <b>Interactive fly</b>, Drosophila genes listed by biochemical function:<br /> [http://www.sdbonline.org/sites/fly/aimain/6biochem.htm Interactive Fly, Thomas Brody and Society for Developmental Biology, MD, USA]
+
* <b>GLAD</b>, an Online Database of Gene List Annotations for Drosophila:<br /> [https://www.flyrnai.org/tools/glad/web/ DRSC/TRiP-FGR, Harvard Medical School, Boston, MA, USA]
* <b>Interactive fly</b>, Maternally transcribed genes:<br /> [http://www.sdbonline.org/sites/fly/aimain/4matrnl.htm Interactive Fly, Thomas Brody and Society for Developmental Biology, MD, USA]
+
* <b>Interactive fly</b>, Drosophila genes listed by biochemical function:<br /> [https://www.sdbonline.org/sites/fly/aimain/6biochem.htm Interactive Fly, Thomas Brody and Society for Developmental Biology, MD, USA]
* <b>Interactive fly</b>, Zygotically transcribed genes:<br /> [http://www.sdbonline.org/sites/fly/aimain/5zygotic.htm Interactive Fly, Thomas Brody and Society for Developmental Biology, MD, USA]
+
* <b>Interactive fly</b>, Maternally transcribed genes:<br /> [https://www.sdbonline.org/sites/fly/aimain/4matrnl.htm Interactive Fly, Thomas Brody and Society for Developmental Biology, MD, USA]
* <b>KEGG BRITE</b>, Functional hierarchies and binary relationships of biological entities:<br /> [http://www.genome.jp/kegg/brite.html KEGG, Kyoto University, Kyoto, Japan and University of Tokyo, Tokyo, Japan]
+
* <b>Interactive fly</b>, Zygotically transcribed genes:<br /> [https://www.sdbonline.org/sites/fly/aimain/5zygotic.htm Interactive Fly, Thomas Brody and Society for Developmental Biology, MD, USA]
 +
* <b>KEGG BRITE</b>, Functional hierarchies and binary relationships of biological entities:<br /> [https://www.genome.jp/kegg/brite.html KEGG, Kyoto University, Kyoto, Japan and University of Tokyo, Tokyo, Japan]
 
* <b>UCSC D. melanogaster Gene Sorter</b>, displays tables of genes related by a variety of characteristics including protein-level homology, similarity of gene expression profiles, and genomic proximity.:<br /> [https://genome.ucsc.edu/cgi-bin/hgNear?org=D.+melanogaster UCSC Genome Informatics Group, University of California, Santa Cruz, Santa Cruz, CA, USA]
 
* <b>UCSC D. melanogaster Gene Sorter</b>, displays tables of genes related by a variety of characteristics including protein-level homology, similarity of gene expression profiles, and genomic proximity.:<br /> [https://genome.ucsc.edu/cgi-bin/hgNear?org=D.+melanogaster UCSC Genome Informatics Group, University of California, Santa Cruz, Santa Cruz, CA, USA]
  
 
=General Bioinformatics Tools=
 
=General Bioinformatics Tools=
* <b>Bioconductor</b>, Open Source Software for Bioinformatics:<br />[http://www.bioconductor.org/ Fred Hutchinson Cancer Research Center, Seattle, USA]
+
* <b>Addgene</b>, Early Career Researcher Toolbox: Free Online Molecular Biology Tools:<br />[https://blog.addgene.org/free-online-molecular-biology-tools Addgene, Watertown, MA, USA]
* <b>BioMart</b>, Data Warehouse:<br />[http://www.biomart.org/ BioMart, EMBL-EBI, OICR, SRSI]
+
* <b>ApE</b>, A plasmid Editor:<br />[https://jorgensen.biology.utah.edu/wayned/ape/ ApE, University of Utah, Salt Lake City, UT, USA]
* <b>Cytoscape</b> -- Network Data Integration, Analysis, and Visualization in a Box:<br />[http://www.cytoscape.org/ Cytoscape, Cytoscape Consortium, Canada, France, and USA]
+
* <b>Bioconductor</b>, Open Source Software for Bioinformatics:<br />[https://www.bioconductor.org/ Fred Hutchinson Cancer Research Center, Seattle, USA]
* <b>DNA & Protein Work List</b>, A list of tools aggregated by the Prokop Lab:<br />[http://www.prokop.co.uk/Links/tools.html http://www.prokop.co.uk/Links/tools.html]
+
* <b>Bioz</b>, Insights and recommendations for products, equipment and assays:<br />[https://www.bioz.com/search/Drosophila Palo Alto, CA, USA]
* <b>FlyMine</b>, an Integrated Database for Drosophila and Anopheles Genomics:<br />[http://www.flymine.org/ University of Cambridge, United Kingdom]
+
* <b>Cytoscape</b> -- Network Data Integration, Analysis, and Visualization in a Box:<br />[https://cytoscape.org/ Cytoscape, Cytoscape Consortium, Canada, France, and USA]
 +
* <b>FlyMine</b>, an Integrated Database for Drosophila and Anopheles Genomics:<br />[https://www.flymine.org/ University of Cambridge, United Kingdom]
 
* <b>FlyNet</b>, 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]
* <b>Galaxy</b>: Open Source Bioinformatics Tools:<br />[https://usegalaxy.org/ Galaxy, Penn State, PA USA and Emory University, GA USA]
+
 
* <b>GSEA</b>, Gene Set Enrichment Analysis:<br />[http://www.broadinstitute.org/gsea/index.jsp GSEA, Broad Institute, Cambridge, MA, USA]
+
=Gene Set Enrichment Analysis=
 +
 
 +
A summary table of selected GSEA tools with information about set up can be found [[FlyBase:GSEA|<b>here</b>]]
 +
 
 +
* <b>DAVID</b>, Database for Annotation, Visualization and Integrated Discovery :<br />[https://david.ncifcrf.gov/ DAVID, Laboratory of Human Retrovirology and Immunoinformatics, Frederick, MD, USA]]
 +
* <b>Enrichr</b>, Human and Mouse Gene Set Enrichment Analysis:<br />[https://maayanlab.cloud/Enrichr/ Enrichr, Center for Bioinfomatics, Mount Sinai, New York, NY, USA]
 +
* <b>MOET</b>, Multi Ontology Enrichment Tool:<br />[https://rgd.mcw.edu/rgdweb/enrichment/start.html MOET, Rat Genome Database]
 +
* <b>modEnrichr</b>, Model Organism Gene Set Enrichment Analysis:<br />[https://maayanlab.cloud/modEnrichr/ modEnrichr, Center for Bioinfomatics, Mount Sinai, New York, NY, USA]
 +
* <b>flyEnrichr</b>, D.melanogaster Gene Set Enrichment Analysis:<br />[https://maayanlab.cloud/FlyEnrichr/ flyEnrichr, Center for Bioinfomatics, Mount Sinai, New York, NY, USA]
 +
* <b>GO term finder</b>, Generic GO Term Finder:<br />[https://go.princeton.edu/cgi-bin/GOTermFinder GOTERMFINDER, Lewis-Sigler Institute for Integrative Genomics, Princeton University, New Jersey, NJ, USA]
 +
* <b>GOC</b>, GO Enrichment Analysis:<br />[https://geneontology.org/ Gene Ontology Consortium]
 +
* <b>GSEA</b>, Gene Set Enrichment Analysis:<br />[https://www.gsea-msigdb.org/gsea/index.jsp GSEA, Broad Institute, Cambridge, MA, USA]
 +
* <b>g:Profiler</b>, g:Profiler/g:GOSt:<br />[https://biit.cs.ut.ee/gprofiler/gost g:Profiler, Institute of Computer Science, University of Tartu, Tartu, Estonia]
 +
* <b>GOrilla</b>, Gene Ontology enRIchment anaLysis and visuaLizAtion tool:<br />[https://cbl-gorilla.cs.technion.ac.il/ GOrilla, Technion, Israel Institute of Technology, Israel]
 +
* <b>PANGEA</b>, PAthway, Network and Gene-set Enrichment Analysis:<br />[https://www.flyrnai.org/tools/pangea/ PANGEA, DRSC, Harvard Medical School, Boston, MA, USA]
 +
* <b>PANTHER</b>, PANTHER GO Enrichment Analysis:<br />[https://pantherdb.org/ PANTHER, University of Southern California, Los Angeles, CA, USA]
 +
* <b>REVIGO</b>, Reduce + Visualize Gene Ontology:<br />[http://revigo.irb.hr/ REVIGO, Division of electronics, Ruđer Bošković Institute, Zagreb, Croatia]
 +
* <b>ShinyGO</b>, ShinyGO 0.80:<br />[http://bioinformatics.sdstate.edu/go80/ ShinyGO, South Dakota State University, Brookings, SD, USA]
 +
* <b>WebGestalt</b>, WebGestalt Gene Set Enrichment Analysis:<br />[https://www.webgestalt.org/  WebGestalt, Baylor College of Medicine, Houston, TX, USA]
  
 
=Genome Sequencing Projects=
 
=Genome Sequencing Projects=
 
* <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]
 
* <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]
* <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]
 
* <b>''D. yakuba'' genome project</b>:<br />[http://genome.wustl.edu/genomes/detail/drosophila-yakuba/ D. yakuba Genome Sequencing Center, Washington University, USA]
 
* <b>D. simulans and yakuba sequencing projects</b>:<br />[http://www.dpgp.org/sim_yak/index.html DPGP, University of California, Davis, USA]
 
  
 
=Human Disease: Drosophila Models and Orthologous Genes=
 
=Human Disease: Drosophila Models and Orthologous Genes=
* <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]
+
* <b>AGR</b> -- Alliance of Genome Resources:<br />[https://www.alliancegenome.org/ Alliance of Genome Resources, RGD, MGD, ZFIN, FlyBase, WormBase, SGD, GO consortium, USA and UK]
 +
* <b>Bloomington Stock Center</b>, Drosophila and Human Disease page:<br />[https://bdsc.indiana.edu/stocks/hd/index.html Bloomington Stock Center, Bloomington, IN, USA]
 
* <b>DIOPT-DIST</b>, Disease-related Ortholog Tool:<br />[http://www.flyrnai.org/cgi-bin/DRSC_DG_query.pl DRSC-TRiP-FGR, 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-TRiP-FGR, Harvard Medical School, Boston, MA, USA]
* <b>Drosophila as a Model for Human Diseases</b>:<br />[http://www.sdbonline.org/sites/fly/modelsystem/aamodelsystem.htm Interactive Fly, Bethesda, MD, USA]
+
* <b>Drosophila as a Model for Human Diseases</b>:<br />[https://www.sdbonline.org/sites/fly/modelsystem/aamodelsystem.htm Interactive Fly, Bethesda, MD, USA]
 
* <b>Drosophila Models of Human Disease</b>, a blog by Stephanie Mohr and Annette Parks:<br />[http://flydiseasemodels.blogspot.com/ flydiseasemodels.blogspot.com/] <br />
 
* <b>Drosophila Models of Human Disease</b>, a blog by Stephanie Mohr and Annette Parks:<br />[http://flydiseasemodels.blogspot.com/ flydiseasemodels.blogspot.com/] <br />
 
* <b>FlyNet Human Disease Prioritization</b>:<br /> [http://www.inetbio.org/flynet/Network_fly_comm.php NetBioLab, Yonsei University, Seoul, Korea]
 
* <b>FlyNet Human Disease Prioritization</b>:<br /> [http://www.inetbio.org/flynet/Network_fly_comm.php NetBioLab, Yonsei University, Seoul, Korea]
* <b>HuDis</b>, high confidence human disease gene - fly gene ortholog pairs:<br />[http://www.flyrnai.org/HuDis DRSC/TRiP-FGR, Harvard Medical School, Boston, MA, USA]
+
* <b>Gene2Function</b>:<br /> [http://www.gene2function.org/search/ Gene2Function, Harvard Medical School, Boston, MA, USA]
 +
* <b>HuDis</b>, high confidence human disease gene - fly gene ortholog pairs:<br />[https://fgr.hms.harvard.edu/hudis-trip-fly-stocks DRSC/TRiP-FGR, Harvard Medical School, Boston, MA, USA]
 +
* <b>MARRVEL</b>, Model organism Aggregated Resources for Rare Variant ExpLoration:<br />[http://marrvel.org/ MARRVEL, Baylor College of Medecine, Houston, TX, USA]
 
* <b>MORPHIN</b>, Model ORganism Projected on a Human Integrated gene Network:<br />[http://www.inetbio.org/morphin/index.php MORPHIN, Lee Lab, Yonsei University, Korea and Marcotte Lab, University of Texas at Austin, USA.]
 
* <b>MORPHIN</b>, Model ORganism Projected on a Human Integrated gene Network:<br />[http://www.inetbio.org/morphin/index.php MORPHIN, Lee Lab, Yonsei University, Korea and Marcotte Lab, University of Texas at Austin, USA.]
* <b>NeuroGeM</b>, A knowledgebase of genetic modifiers in neurodegenerative diseases:<br />[http://chibi.ubc.ca/neurogem/ CHiBi, The University of British Columbia, Vancouver, BC, Canada]
 
  
 
=Interaction and Pathway Databases=
 
=Interaction and Pathway Databases=
* <b>BioGRID</b>, The General Repository for Interaction Datasets:<br />[http://www.thebiogrid.org/index.php BioGRID, Mount Sinai Hospital, Toronto, Canada]
+
* <b>BioCyc - FLY</b> -- Curated Drosophila melanogaster Pathways:<br />[https://biocyc.org/FLY/organism-summary?object=FLY FlyCyc, Harvard University, Cambridge, USA]
* <b>COMPLEAT</b>, protein COMPLex Enrichment Analysis Tool:<br />[http://www.flyrnai.org/compleat/ COMPLEAT, DRSC, Harvard Medical School, Boston, MA, USA]
+
* <b>BioGRID</b>, The General Repository for Interaction Datasets:<br />[https://thebiogrid.org/index.php BioGRID, Mount Sinai Hospital, Toronto, Canada]
* <b>DAPPER</b>, database for protein-protein interactions:<br/>[http://dapper.gen.cam.ac.uk/ DAPPER, University of Cambridge, Cambridge, UK]
+
* <b>COMPLEAT</b>, protein COMPLex Enrichment Analysis Tool:<br />[https://www.flyrnai.org/compleat/ COMPLEAT, DRSC, Harvard Medical School, Boston, MA, USA]
* <b>DPiM</b>, Drosophila Protein interaction Map:<br />[https://interfly.med.harvard.edu/ DPiM, Harvard University Medical School, Boston, MA, USA]
+
* <b>DPiM</b>, Drosophila Protein interaction Map:<br/>[https://interfly.med.harvard.edu/ DPiM, Harvard University Medical School, Boston, MA, USA]
 
* <b>DroID</b>, Drosophila Interactions Database:<br />[http://www.droidb.org/ Drosophila Interaction Database, Detroit, USA]
 
* <b>DroID</b>, Drosophila Interactions Database:<br />[http://www.droidb.org/ Drosophila Interaction Database, Detroit, USA]
* <b>Drosophila PIMRider</b>, Drosophila Protein Interaction Map:<br />[https://pimr.hybrigenics.com/htmlFiles/interactionData/drosophila.html Drosophila PIMRider, Hybrigenics, Paris, France]
+
* <b>FlyBase Signaling Pathways</b>, Manually curated reports on Signaling Pathways, based on the literature:<br /> [http://flybase.org/lists/FBgg/pathways Pathways list, FlyBase]
* <b>FlyCyc</b> -- Curated Drosophila melanogaster Pathways:<br />[http://biocyc.org/FLY/organism-summary?object=FLY FlyCyc, Harvard University, Cambridge, USA]
 
 
* <b>FlyNet Gene Prioritization</b>: <br /> [http://www.inetbio.org/flynet/Network_gene_prioritization.php NetBioLab, Yonsei University, Seoul, Korea]
 
* <b>FlyNet Gene Prioritization</b>: <br /> [http://www.inetbio.org/flynet/Network_gene_prioritization.php NetBioLab, Yonsei University, Seoul, Korea]
 
* <b>FlyOde</b>, FLY Organ Developmental Network: <br /> [http://flyode.boun.edu.tr/index.html FlyOde, Bogazici University, Istanbul, Turkey]
 
* <b>FlyOde</b>, FLY Organ Developmental Network: <br /> [http://flyode.boun.edu.tr/index.html FlyOde, Bogazici University, Istanbul, Turkey]
* <b>FlyReactome</b> -- a Curated Knowledgebase of Drosophila melanogaster Pathways:<br />[http://fly.reactome.org FlyReactome, University of Cambridge, Cambridge, UK]
+
* <b>HOMER</b>, Software for motif discovery and next-gen sequencing analysis: <br /> [http://homer.ucsd.edu/homer/motif/ HOMER, University of California at San Diego, San Diego, CA, USA]
 
* <b>IM Browser</b>, Drosophila Interactions Database:<br />[http://proteome.wayne.edu/PIMdb.html IM Browser, Wayne State University, Detroit, MI, USA]
 
* <b>IM Browser</b>, Drosophila Interactions Database:<br />[http://proteome.wayne.edu/PIMdb.html IM Browser, Wayne State University, Detroit, MI, USA]
* <b>IntAct</b>, Molecular Interaction Database:<br />[http://www.ebi.ac.uk/intact/ IntAct, EMBL-EBI, Hinxton, UK]
+
* <b>IntAct</b>, Molecular Interaction Database:<br />[https://www.ebi.ac.uk/intact/ IntAct, EMBL-EBI, Hinxton, UK]
* <b>KEGG</b> -- Kyoto Encyclopedia of Genes and Genomes:<br />[http://www.genome.jp/kegg KEGG, Kyoto, Japan]
+
* <b>KEGG</b> -- Kyoto Encyclopedia of Genes and Genomes:<br />[https://www.genome.jp/kegg/ KEGG, Kyoto, Japan]
* <b>Reactome Pathway Database</b>:<br />[http://www.reactome.org/ Reactome, OICR, Ontario, Canada, EMBL-EBI, UK, NYU Medical Center, NY, USA]
+
* <b>MIST</b> -- Molecular Interactions Search Tool:<br />[https://fgrtools.hms.harvard.edu/MIST/ MIST, Harvard Medical School, Boston, MA, USA]
* <b>SignaLink</b>, A signaling pathway resource with multi-layered regulatory networks:<br />[http://http://signalink.org/ SignaLink, Eötvös Loránd University of Science, Budapest, Hungary]
+
* <b>Reactome Pathway Database</b>:<br />[https://reactome.org/ Reactome, OICR, Ontario, Canada, EMBL-EBI, UK, NYU Medical Center, NY, USA]
* <b>SignedPPI</b>, Searchable Database of Known and Predicted Protein-protein Interactions:<br />[http://www.flyrnai.org/SignedPPI/ DRSC, Harvard Medical School, Boston, MA, USA]
+
* <b>SignaLink</b>, an integrated resource to analyze signaling pathway cross-talks, transcription factors, miRNAs and regulatory enzymes.:<br />[http://signalink.org/ SignaLink, Earlham Institute, Norwich, UK]
* <b>STRING</b>, Known and Predicted Protein-Protein Interactions<br />[http://string-db.org/ STRING, SIB, Switzerland CPR, Denmark, and EMBL, Heidelberg, Germany]
+
* <b>STRING</b>, Known and Predicted Protein-Protein Interactions<br />[https://string-db.org/ STRING, SIB, Switzerland CPR, Denmark, and EMBL, Heidelberg, Germany]
* <b>WikiPathways</b>, an open, public platform dedicated to the curation of biological pathways by and for the scientific community:<br />[http://www.wikipathways.org/index.php/WikiPathways WikiPathways, Gladstone Institute, San Francisco, CA, USA and Maastricht University, The Netherlands]
+
* <b>WikiPathways</b>, an open, public platform dedicated to the curation of biological pathways by and for the scientific community:<br />[https://www.wikipathways.org/index.php/WikiPathways WikiPathways, Gladstone Institute, San Francisco, CA, USA and Maastricht University, The Netherlands]
  
=Laboratory Resources=
+
=Metabolomics=
* <b>Laboratory Manual of Drosophila</b>: <br />[http://darwin.bio.uci.edu/~mueller/pdf/Lab_manual.pdf PDF, Chippindale, A. ''et al''., Department of Ecology & Evolutionary Biology, University of California, Irvine, USA]
+
* <b>FlyMet</b>, A Tissue- and Sex-Specific Metabolomic Atlas and Database :<br />[http://www.flymet.org/ FlyMet, University of Glasgow, Glasgow, Scotland]
  
 
=Miscellaneous=
 
=Miscellaneous=
 +
* <b>AGR</b> -- Alliance of Genome Resources:<br />[https://www.alliancegenome.org/ Alliance of Genome Resources, RGD, MGD, ZFIN, FlyBase, WormBase, SGD, GO consortium, USA and UK]
 +
* <b>BioLitMine</b>, Biological Literature Mining Tool for Human and Model Organisms:<br />[https://www.flyrnai.org/tools/biolitmine/web/ BioLitMine, Harvard Medical School, Boston, MA, USA]
 
* <b>Bionet Archives</b>, a collection of bionet USENET newsgroups and parallel e-mail lists regarding Drosophila:<br />[http://www.bio.net/hypermail/dros/ Genome Informatics Lab, Indiana University, Bloomington, Indiana, USA]
 
* <b>Bionet Archives</b>, a collection of bionet USENET newsgroups and parallel e-mail lists regarding Drosophila:<br />[http://www.bio.net/hypermail/dros/ Genome Informatics Lab, Indiana University, Bloomington, Indiana, USA]
* <b>DOR</b>, Database of Olfactory Receptors:<br />[http://caps.ncbs.res.in/DOR/index.html DOR, NCBS, Bangalore, India, AIST, Tokyo, Japan]
+
* <b>Drosophila App</b>, A mobile application developed by Genesee for use in fly research: <br />[https://play.google.com/store/apps/details?id=kaver.co.drosophila&hl=en Android]
* <b>Drosophila App</b>, A mobile application developed by Genesee for use in fly research: <br />[https://itunes.apple.com/us/app/drosophila/id626253408?mt=8 iTunes] | [https://play.google.com/store/apps/details?id=kaver.co.drosophila&hl=en Android]
+
* <b>Drosophila Information Service</b>:<br />[https://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]
+
* <b>Drosophila Species Photographs</b>, Photographs of 133 species of Drosophila:<br />[https://kyotofly.kit.jp/cgi-bin/ehime/photo_data_list.cgi Ehime University, Matsuyama, Japan]
* <b>Fly Labs and References</b>, a large list of fly labs and recent publications: <br />[http://www.sdbonline.org/sites/fly/flylabs/a.html Interactive Fly, Bethesda, MD, USA]
+
* <b>Drosophila Workers Unite! A laboratory manual for working with Drosophila</b>:<br />[https://marksteinlab.org/dwu/ Michele Markstein Lab, UMass Amherst, Amherst, MA, USA]
* <b>FlyTree</b>, the Drosophila Researcher Genealogy has been incorporated into the Academic Tree Project: <br />[http://www.academictree.org/flytree/ FlyTree, USA]
+
* <b>The Encyclopedia of North American Drosophilids Volume 1: Drosophilids of the Midwest and Northeast</b>:<br />[https://digitalcommons.mtu.edu/oabooks/1/ by T. Werner, Michigan Technological University, Tessa Steenwinkel, Michigan Technological University, and J.Jaenike, University of Rochester]
* <b>GenAge</b> -- The Ageing Gene Database:<br />[http://genomics.senescence.info/genes/ Human Ageing Genomic Resources, Institute of Integrative Biology, Liverpool, UK]
+
* <b>Fly Art</b> - A compendium of arty imagery, sculptures or poetry inspired by Drosophila or flies in the wider sense.:<br />[https://droso4public.wordpress.com/fly-art/ University of Manchester, Manchester, UK]
* <b>Gene Lookup</b>, Gene and Reagent Lookup:<br />[http://www.flyrnai.org/cgi-bin/DRSC_gene_lookup.pl Gene Lookup, DRSC, Harvard Medical School, Boston, MA, USA]
+
* <b>Fly Labs and References</b>, a large list of fly labs and recent publications: <br />[https://www.sdbonline.org/sites/fly/flylabs/a.html Interactive Fly, Bethesda, MD, USA]
* <b>IGTRCN</b>, Insect Genetic Technologies Research Coordination Network:<br />[http://igtrcn.org// IGTRCN, University of Maryland, Rockville, MD, USA]
+
* <b>FlyTree</b>, the Drosophila Researcher Genealogy has been incorporated into the Academic Tree Project: <br />[https://academictree.org/flytree/ FlyTree, USA]
* <b>Interactive Fly</b>, A cyberspace guide to Drosophila development and metazoan evolution<br />[http://www.sdbonline.org/fly/aimain/1aahome.htm Interactive Fly, Bethesda, MD, USA]
+
* <b>Fully automated drosophila wing landmarking</b>, Automatically finds more than 110 landmark points and creates a digital twin of the drosophila wing:<br />[https://datamarkin.com/models/drosophila-wings-beta/ Datamarkin, Marseille, France]
* <b>Jfly</b>, a data depository for the fly and other insects, with an emphasis for the Japanese-speaking fly community:<br />[http://jfly.iam.u-tokyo.ac.jp/ Jfly, University of Tokyo, Japan]
+
* <b>GenAge</b> -- The Ageing Gene Database:<br />[https://genomics.senescence.info/genes/index.html Human Ageing Genomic Resources, Institute of Integrative Biology, Liverpool, 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]
+
* <b>Gene Lookup</b>, Gene and Reagent Lookup:<br />[https://www.flyrnai.org/cgi-bin/DRSC_gene_lookup.pl Gene Lookup, DRSC, Harvard Medical School, Boston, MA, USA]
* <b>MitoDrome</b>, ''Drosophila melanogaster'' nuclear genes encoding for mitochondrial proteins:<br />[http://mitodrome.ba.itb.cnr.it/ MitoDrome, Bari, Italy]
+
* <b>GlyCosmos Portal</b>, a Web portal aiming to integrate the glycosciences with the life sciences. It consists of Standards, Repositories and Data Resources, providing information about genes, proteins, lipids, pathways and diseases.:<br />[https://glycosmos.org/ GlyCosmos, GlyCosmos is a member of the GlySpace Alliance, consisting of ExPASy Glycomics, GlyCosmos, and GlyGen]
* <b>Mitotic Spindle Assembly Database</b>:<br />[http://rnai.ucsf.edu/mitospindlescreen/index.html Genes Required for Mitotic Spindle Assembly in S2 cells, University of California, San Francisco, USA]
+
* <b>Interactive Fly</b>, A cyberspace guide to Drosophila development and metazoan evolution<br />[https://www.sdbonline.org/sites/fly/aimain/1aahome.htm Interactive Fly, Bethesda, MD, USA]
 +
* <b>Manchester Fly Facility, Resources</b> - A compendium of information on ''Drosophila melanogaster'' as a model organism:<br />[https://droso4public.wordpress.com/resources/ University of Manchester, Manchester, UK]
 
* <b>Multiplex Fluorescent mRNA <em>In Situ</em> Hybridization</b>, information on how to perform multiplex fluorescent mRNA in situ hybridization on Drosophila embryos: <br />[http://people.biology.ucsd.edu/davek/ Bier and McGinnis Labs, UCSD, San Diego, California, USA]
 
* <b>Multiplex Fluorescent mRNA <em>In Situ</em> Hybridization</b>, information on how to perform multiplex fluorescent mRNA in situ hybridization on Drosophila embryos: <br />[http://people.biology.ucsd.edu/davek/ Bier and McGinnis Labs, UCSD, San Diego, California, USA]
* <b>PhenomicDB</b>, A Cross-species Genotype-Phenotype Resource:<br />[http://phenomicdb.de/ Phenotype-Genotype Database, Berlin, Germany]
+
* <b>What's hot today:</b> Current papers in developmental biology and gene function:<br />[https://www.sdbonline.org/sites/fly/aimain/model-organisms-this-week.htm Interactive Fly, Bethesda, MD, 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.]
+
* <b>The WWW Virtual Library--Drosophila</b>:<br />[https://www.ceolas.org/fly/ Drosophila Virtual Library]
* <b>What's hot today:</b> Current papers in developmental biology and gene function:<br />[http://www.sdbonline.org/sites/fly/aimain/model-organisms-this-week.htm Interactive Fly, Bethesda, MD, USA]
+
 
* <b>The WWW Virtual Library--Drosophila</b>:<br />[http://www.ceolas.org/fly/ Drosophila Virtual Library]
+
=Non-coding (ncRNA) Databases and Tools=
  
=ncRNA Databases and Tools=
+
==General==
* <b>DIANA microT-CDS</b>, MicroRNA Target Prediction:<br />[http://diana.imis.athena-innovation.gr/DianaTools/index.php?r=microT_CDS/index DIANA microT-CDS, DIANA LAB, Athens, Greece]
+
* <b>NONCODE</b>, An integrated knowledge database dedicated to ncRNAs, especially lncRNAs:<br />[http://www.noncode.org/ NONCODE, Tsinghua University and Chinese Academy of Sciences, Beijing, China]
* <b>DIANA TarBase</b>, MicroRNA Target Database:<br />[http://diana.imis.athena-innovation.gr/DianaTools/index.php?r=tarbase/index DIANA TarBase, DIANA LAB, Athens, Greece]
+
* <b>Rfam</b>, A collection of RNA sequence families of structural RNAs including non-coding RNA genes as well as cis-regulatory elements :<br />[https://rfam.org/ Rfam, EMBL-EBI, Hinxton, UK]
* <b>GtRNAdb</b>, tRNAscan-SE analysis of complete genomes:<br />[http://gtrnadb.ucsc.edu/ GtRNAdb, Lowe lab, University of California, Santa Cruz, Santa Cruz, CA, USA]
+
* <b>RNAcentral</b>, Integrated access to a comprehensive and up-to-date set of non-coding RNA sequences provided by a collaborating group of Expert Databases :<br />[https://rnacentral.org/ RNAcentral, EMBL-EBI, Hinxton, UK]
* <b>MinoTar</b>, Predict microRNA Targets in Coding Sequence:<br />[http://www.flyrnai.org/cgi-bin/DRSC_MinoTar.pl MinoTar, DRSC, Harvard Medical School, Boston, MA, USA]
+
 
* <b>miRBase</b>, microRNA data:<br />[http://www.mirbase.org/ miRBase, University of Manchester, UK]
+
==lncRNA==
 +
* <b>LncRBase V.2</b>, a database of information about lncRNAs from 8 species (human, mouse, fly, zebrafish, rat, chicken, C.elegans and cow) :<br />[http://dibresources.jcbose.ac.in/zhumur/lncrbase2/index_Contact.php LncRBase, Bose Institute, West Bengal, India]
 +
 
 +
==miRNA==
 +
===General===
 +
* <b>miRBase</b>, A searchable database of published miRNA sequences and annotations (current miBase release is 22 - last updated 2018):<br />[https://mirbase.org/// miRBase, University of Manchester, UK]<br />
 
::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.
* <b>miRNA, Target Gene Prediction</b>:<br />[http://www.mirna.embl.de/ miRNA - Target Prediction, EMBL, Heidelberg, Germany]
+
* <b>miRNEST</b>, An integrated collection of miRNA predictions from high-throughput sequencing experiments and external database annotations (last updated 2015):<br />[http://rhesus.amu.edu.pl/mirnest/copy/ miRNEST, The Adam Mickiewicz University in Poznan, Poznan, Poland]
* <b>miRNA_Targets</b>:<br />[http://mamsap.it.deakin.edu.au/~amitkuma/mirna_targetsnew/index.html miRNA targets on full length mRNAs, Deakin University, Victoria, Australia]
+
* <b>TransmiR</b>, A database of transcription factor-microRNA regulation (last updated 2018):<br />[http://www.cuilab.cn/transmir TransmiR], Peking University Health Science Center, Peking, Chin
* <b>miRTarBase</b>, Experimentally Validated microRNA-target Interactions Database:<br />[http://mirtarbase.mbc.nctu.edu.tw/ miRTarBase, ISBLab, Hsinchu, Taiwan]
+
 
* <b>Rfam</b>, RNA families database of alignments and CMs:<br />[http://www.webcitation.org/getfile?fileid=db1c351a4c279e9cf9697bd2d1962097900701fb Rfam, Wellcome Trust Sanger Institute, Hinxton, UK and Janelia Farm, Ashburn, VA, USA]
+
===miRNA Target Prediction===
* <b>RNAcentral</b>, provides unified access to the ncRNA sequence data supplied by multiple Expert Databases:<br />[http://rnacentral.org/ RNAcentral, EMBL-EBI, Hingston, UK]
+
* <b>DIANA microT-CDS</b>, MicroRNA Target Prediction:<br />[https://dianalab.e-ce.uth.gr/html/dianauniverse/index.php?r=microT_CDS DIANA Tools, DIANA LAB, Athens, Greece]
 +
* <b>MinoTar</b>, Predict microRNA Targets in Coding Sequence (last updated 2010):<br />[https://www.flyrnai.org/cgi-bin/DRSC_MinoTar.pl MinoTar, DRSC, Harvard Medical School, Boston, MA, USA]
 +
* <b>TargetScanFly</b>, Prediction of microRNA targets based on miRNA seed region and target conservation (last updated 2012):<br />[https://www.targetscan.org/fly_12/ TargetScanFly, Whitehead Institute and MIT Dept. of Biology, Cambridge, MA, USA]
 +
 
 +
===Validated miRNA Targets===
 +
* <b>DIANA TarBase</b>, MicroRNA Target Database (last updated 2017):<br />[https://dianalab.e-ce.uth.gr/html/diana/web/index.php?r=tarbasev8 DIANA TarBase, DIANA LAB, Athens, Greece]
 +
* <b>miRTex</b>, A text-mining system that extracts miRNA-gene regulation relations and miRNA-target relations from literature (last updated 2017):<br />[https://research.bioinformatics.udel.edu/miRTex/ miRTex, University of Delaware, Newark, DE, USA]
 +
 
 +
===Comparative miRNA Analysis===
 +
* <b>microRNAviewer</b>, A global view of homologous miRNA genes in many species (last updated 2012):<br />[http://people.csail.mit.edu/akiezun/microRNAviewer/index.html microRNAviewer, Tel Aviv University, Tel Aviv, Israel]
 +
 
 +
==rRNA==
 +
* <b>SILVA</b>, High quality ribosomal RNA databases (last updated 2020):<br />[https://www.arb-silva.de/ SILVA, Max Planck Institute for Marine Microbiology and Jacobs University, Bremen, Germany]
 +
 
 +
==tRNA==
 +
* <b>tRFdb</b>, A relational database of Transfer RNA related Fragments:<br />[http://genome.bioch.virginia.edu/trfdb/index.php tRFdb, Dutta lab, University of Virginia, Charlottesville, VA, USA]
 +
 
 +
==snoRNA==
 
* <b>snOPY</b>, a snoRNA orthological gene database providing comprehensive information about snoRNAs, snoRNA gene loci and target RNAs.:<br />[http://snoopy.med.miyazaki-u.ac.jp/ snOPY, University of Miyazaki, Japan ]
 
* <b>snOPY</b>, a snoRNA orthological gene database providing comprehensive information about snoRNAs, snoRNA gene loci and target RNAs.:<br />[http://snoopy.med.miyazaki-u.ac.jp/ snOPY, University of Miyazaki, Japan ]
* <b>TargetScanFly</b>, Prediction of microRNA targets:<br />[http://www.targetscan.org/fly_12/ TargetScanFly, Whitehead Institute and MIT Dept. of Biology, USA]]
+
==SRP RNA==
 +
* <b>SRPDB</b>, Signal Recognition Particle Database:<br />[http://rth.dk/resources/rnp/SRPDB/SRPDB.html SRPDB, University of Texas Health Science Center, San Antonio, USA]
  
 
=Ontology Resources=
 
=Ontology Resources=
* <b>AmiGO 2</b>, tools for searching and browsing the Gene Ontology database:<br />[http://amigo2.berkeleybop.org/amigo AmiGO 2, Berkeley Bioinformatics Open-source Projects, USA]
 
 
* <b>BioPortal</b>, a biomedical ontologies repository and browser:<br />[http://bioportal.bioontology.org/ BioPortal, The National Center for Biomedical Ontology, USA]
 
* <b>BioPortal</b>, a biomedical ontologies repository and browser:<br />[http://bioportal.bioontology.org/ BioPortal, The National Center for Biomedical Ontology, USA]
* <b>Disease Ontology</b>, ontology of disease terms:<br />[http://disease-ontology.org/ Disease Ontology]
+
* <b>Disease Ontology (DO)</b>, ontology of disease terms:<br />[http://disease-ontology.org/ Disease Ontology]
* <b>Gene Ontology Consortium</b><br />[http://geneontology.org/ Gene Ontology Consortium]
+
* <b>Gene Ontology Consortium (GO)</b><br />[https://geneontology.org/ Gene Ontology Consortium]
* <b>GOrilla</b> -- Gene Ontology enRIchment and anaLysis and viuaLizAtion tool:<br />[http://cbl-gorilla.cs.technion.ac.il/ GOrilla, Israel]
+
* <b>GOrilla</b> -- Gene Ontology enRIchment and anaLysis and viuaLizAtion tool:<br />[https://cbl-gorilla.cs.technion.ac.il/ GOrilla, Israel]
 
* <b>OboEdit</b>, browser for OBO ontologies:<br />[http://oboedit.org/ OboEdit]
 
* <b>OboEdit</b>, browser for OBO ontologies:<br />[http://oboedit.org/ OboEdit]
* <b>The OBO Foundry</b>, an ontology registry:<br />[http://obofoundry.github.io/ OboFoundry]
+
* <b>The OBO Foundry</b>, an ontology registry:<br />[http://obofoundry.org/ OboFoundry]
* <b>Ontobee</b>, an ontologies browser:<br />[http://www.ontobee.org/ Ontobee, He Group, University of Michigan Medical School, Ann Arbor, Michigan, USA]
+
* <b>Ontobee</b>, an ontologies browser:<br />[https://ontobee.org/ Ontobee, He Group, University of Michigan Medical School, Ann Arbor, Michigan, USA]
* <b>Ontology Lookup Service</b>, an ontologies browser:<br />[http://www.ebi.ac.uk/ontology-lookup/ Ontology Lookup Service, EMBL-EBI, Hinxton, UK]
+
* <b>OLS - Ontology Lookup Service</b>, an ontologies browser:<br />[https://www.ebi.ac.uk/ols4/ Ontology Lookup Service, EMBL-EBI, Hinxton, UK]
* <b>Protege</b>, browser for OWL ontologies:<br />[http://protege.stanford.edu/products.php, Protege, Stanford Center for Biomedical Informatics Research, Stanford University School of Medicine, USA]
+
* <b>Protege</b>, browser for OWL ontologies:<br />[https://protege.stanford.edu/ Protege, Stanford Center for Biomedical Informatics Research, Stanford University School of Medicine, USA]
* <b>QuickGO</b>, a browser for Gene Ontology terms and annotations:<br />[http://www.ebi.ac.uk/QuickGO/ QuickGO, EMBL-EBI, Hinxton, UK]
+
* <b>QuickGO</b>, a browser for Gene Ontology terms and annotations:<br />[https://www.ebi.ac.uk/QuickGO/ QuickGO, EMBL-EBI, Hinxton, UK]
  
 
=Orthology Predictions=
 
=Orthology Predictions=
 
* <b>Compara</b>, Ensembl Compara provides cross-species resources and analyses, at both the sequence level and the gene level.<br />[http://useast.ensembl.org/info/genome/compara/index.html?redirect=no Ensembl, Hinxton, UK]
 
* <b>Compara</b>, Ensembl Compara provides cross-species resources and analyses, at both the sequence level and the gene level.<br />[http://useast.ensembl.org/info/genome/compara/index.html?redirect=no Ensembl, Hinxton, UK]
* <b>DIOPT</b>, DRSC Integrative Ortholog Prediction Tool<br />[http://www.flyrnai.org/cgi-bin/DRSC_orthologs.pl DRSC/TRiP-FGR, Harvard Medical School, Boston, MA, USA]
+
* <b>DIOPT</b>, DRSC Integrative Ortholog Prediction Tool<br />[https://www.flyrnai.org/cgi-bin/DRSC_orthologs.pl DRSC/TRiP-FGR, Harvard Medical School, Boston, MA, USA]
* <b>DIOPT-DIST: DIOPT Diseases and Traits</b>, DRSC Disease Gene Query Tool:<br />[http://www.flyrnai.org/cgi-bin/DRSC_DG_query.pl DRSC/TRiP-FGR, Harvard Medical School, Boston, MA, USA]
+
* <b>DIOPT-DIST: DIOPT Diseases and Traits</b>, DRSC Disease Gene Query Tool:<br />[https://www.flyrnai.org/cgi-bin/DRSC_DG_query.pl DRSC/TRiP-FGR, Harvard Medical School, Boston, MA, USA]
* <b>EggNOG</b>, A database of orthologous groups and functional annotation:<br />[http://eggnogdb.embl.de/#/app/home Computational Biology Group, EMBL, Heidelberg, Germany]
+
* <b>EggNOG</b>, A database of orthologous groups and functional annotation:<br />[http://eggnogdb.embl.de/ Computational Biology Group, EMBL, Heidelberg, Germany]
* <b>Homologene</b>, An automated system for constructing putative homology groups from the complete gene sets of a wide range of eukaryotic species.<br />[http://www.ncbi.nlm.nih.gov/homologene NCBI, Bethesda, MD, USA]
+
* <b>Gene2Function</b>:<br /> [https://www.gene2function.org/search/ Gene2Function, Harvard Medical School, Boston, MA, USA]
* <b>Inparanoid</b>, InParanoid: ortholog groups with inparalogs<br />[http://inparanoid.sbc.su.se/cgi-bin/index.cgi Stockholm Bioinformatics Centre, Stockholm, Sweden]
+
* <b>Hieranoid</b>, An orthology inference method using a hierarchical approach. Hieranoid performs pairwise orthology analysis using InParanoid at each node in a guide tree as it progresses from its leaves to the root.<br />[https://hieranoid.sbc.su.se/index.html Hieranoid, Stockholm Bioinformatics Centre, Stockholm, Sweden]
* <b>Isobase</b>, A Database of Functionally Related Orthologs, which incorporates PPI network data in addition to sequence similarity.<br />[http://groups.csail.mit.edu/cb/mna/isobase/ MIT, Cambridge, MA, USA]
+
* <b>HieranoiDB</b>, An online database of orthologs inferred by Hieranoid 2 for a representative set of proteomes.<br />[https://hieranoidb.sbc.su.se/ HieranoiDB, Stockholm Bioinformatics Centre, Stockholm, Sweden]
* <b>OMA Browser</b>, The OMA (“Orthologous MAtrix”) project is a method and database for the inference of orthologs among complete genomes.<br />[http://omabrowser.org/oma/home/ Nucl. Acids Res. 43 (D1): D240-D249. doi: 10.1093/nar/gku1158]
+
* <b>Homologene</b>, An automated system for constructing putative homology groups from the complete gene sets of a wide range of eukaryotic species.<br />[https://www.ncbi.nlm.nih.gov/datasets/gene/ NCBI, Bethesda, MD, USA]
* <b>OrthoDB</b>, The Hierarchical Catalog of Orthologs<br />[http://orthodb.org/ Zdobnov Computational Evolutionary Genomics group, University of Geneva, Geneva, Switzerland]
+
* <b>InParanoiDB 9</b>, Ortholog groups with inparalogs for proteins and protein domains<br />[https://inparanoidb.sbc.su.se/about/ InParanoiDB 9, Stockholm Bioinformatics Centre, Stockholm, Sweden]
* <b>OrthoMCL</b>, Ortholog Groups of Protein Sequences<br />[http://www.orthomcl.org/orthomcl/ EuPathDB]
+
* <b>Isobase</b>, A Database of Functionally Related Orthologs, which incorporates PPI network data in addition to sequence similarity.<br />[http://cb.csail.mit.edu/cb/mna/isobase/ MIT, Cambridge, MA, USA]
 +
* <b>MARRVEL</b>, Model organism Aggregated Resources for Rare Variant ExpLoration:<br />[http://marrvel.org/ MARRVEL, Baylor College of Medecine, Houston, TX, USA]
 +
* <b>OMA Browser</b>, The OMA (“Orthologous MAtrix”) project is a method and database for the inference of orthologs among complete genomes.<br />[https://omabrowser.org/oma/home/ Nucl. Acids Res. 43 (D1): D240-D249. doi: 10.1093/nar/gku1158]
 +
* <b>OrthoDB</b>, The Hierarchical Catalog of Orthologs<br />[https://www.orthodb.org/ Zdobnov Computational Evolutionary Genomics group, University of Geneva, Geneva, Switzerland]
 +
* <b>OrthoFinder</b>, A comprehensive platform for comparative genomics that finds orthogroups and orthologs, infers rooted gene trees for all orthogroups and identifies all of the gene duplication events.<br />[http://www.stevekellylab.com/software/orthofinder University of Oxford, Oxford, UK]
 +
* <b>OrthoInspector</b>, A software suite for inference of orthologous relationships between protein coding-genes and an online resource to access and query precomputed orthology databases.<br />[https://lbgi.fr/orthoinspector/ ICube Laboratory, Graffenstaden, France]
 +
* <b>OrthoMCL</b>, Ortholog Groups of Protein Sequences<br />[https://orthomcl.org/orthomcl/ EuPathDB]
 
* <b>PANTHER</b>, PANTHER Classification System<br />[http://pantherdb.org/genes/ Thomas Lab, University of Southern California, Los Angeles, CA, USA]
 
* <b>PANTHER</b>, PANTHER Classification System<br />[http://pantherdb.org/genes/ Thomas Lab, University of Southern California, Los Angeles, CA, USA]
 
* <b>PhylomeDB</b>, PhylomeDB is a public database for complete catalogs of gene phylogenies (phylomes)<br />[http://phylomedb.org/ Comparative Genomics Groups at CRB, Barcelona, Spain]
 
* <b>PhylomeDB</b>, PhylomeDB is a public database for complete catalogs of gene phylogenies (phylomes)<br />[http://phylomedb.org/ Comparative Genomics Groups at CRB, Barcelona, Spain]
* <b>Roundup</b>, A large-scale orthology database using the Reciprocal Smallest Distance (RSD) algorithm.<br />[http://wall-lab.stanford.edu/projects/roundup/ Wall lab, Stanford University, Palo Alto, CA, USA]
+
* <b>Roundup</b>, A large-scale orthology database using the Reciprocal Smallest Distance (RSD) algorithm.<br />[https://wall-lab.stanford.edu/projects/roundup/ Wall lab, Stanford University, Palo Alto, CA, USA]
 
* <b>TreeFam</b>, A database composed of phylogenetic trees inferred from animal genomes. It provides orthology/parology predictions as well the evolutionary history of genes.<br />[http://www.treefam.org/ EMBL-EBI, Hinxton, UK]
 
* <b>TreeFam</b>, A database composed of phylogenetic trees inferred from animal genomes. It provides orthology/parology predictions as well the evolutionary history of genes.<br />[http://www.treefam.org/ EMBL-EBI, Hinxton, UK]
  
 
=Phylogenetic Comparison Tools=
 
=Phylogenetic Comparison Tools=
* <b>Assembly/Alignment/Annotation of 12 related ''Drosophila'' species</b>:<br />[http://rana.lbl.gov/drosophila/ Assembly/Alignment/Annotation, LBNL, USA]
+
* <b>DIOPT</b>, DRSC Integrative Ortholog Prediction Tool:<br />[https://www.flyrnai.org/cgi-bin/DRSC_orthologs.pl DRSC/TRiP-FGR, 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/TRiP-FGR, Harvard Medical School, Boston, MA, USA]
+
* <b>HomoloGene</b> -- automated system fo constructing putative homology groups:<br />[https://www.ncbi.nlm.nih.gov/datasets/gene/ NCBI, Bethesda, MA, USA]
* <b>EvoPrinter</b>, Identification of Evolutionarily Resilient DNA Sequences<br />[http://evoprinter.ninds.nih.gov/ NINDS, NIH, Bethesda MD, USA]
+
* <b>InParanoiDB 9</b>, Ortholog groups with inparalogs for proteins and protein domains<br />[https://inparanoidb.sbc.su.se/about/ InParanoiDB 9, Stockholm Bioinformatics Centre, Stockholm, Sweden]
* <b>HomoloGene</b> -- automated system fo constructing putative homology groups:<br />[http://www.ncbi.nlm.nih.gov/homologene NCBI, Bethesda, MA, USA]
+
* <b>MANTiS</b>, a phylogenetic framework for multi-species genome comparisons:<br />[https://www.mantisdb.org/MANTiS/Welcome.html MANTiS, Université Libre de Bruxelles, Belgium]
* <b>InParanoid</b>, Eukaryotic Ortholog Groups:<br />[http://inparanoid.sbc.su.se/cgi-bin/index.cgi InParanoid, Karolinska Institute, Sweden]
+
* <b>OrthoDB</b>, the Hierarchical Catalog of Orthologs:<br />[http://www.orthodb.org/ OrthoDB, University of Geneva, Switzerland]
* <b>MANTiS</b>, a phylogenetic framework for multi-species genome comparisons:<br />[http://www.mantisdb.org/MANTiS/Welcome.html MANTiS, Université Libre de Bruxelles, Belgium]
+
* <b>Vista Tools</b> -- Whole Genome Comparative Analysis of the ''D. melanogaster'' (CAF1) Genome:<br />[https://pipeline.lbl.gov/cgi-bin/gateway2?bg=droMel_caf1&selector=vistapoint Whole Genome Comparative Analysis of the D. melanogaster (CAF1) Genome, LBNL, USA]
* <b>OrthoDB</b>, the Hierarchical Catalog of Orthologs:<br />[http://orthodb.org/orthodb7 OrthoDB, University of Geneva, Switzerland]
 
* <b>flyDIVaS</b>, a comparative genomics database resource of ''Drosophila'' divergence and selection: <br />[http://flydivas.info/ Temple University, Philadelphia, PA, 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=
* <b>BDGP Single Nucleotide Polymorphism (SNP) Project</b>:<br />[http://www.fruitfly.org/SNP/ Berkeley Drosophila Genome Project, University of California, Berkeley, USA]
+
* <b>BDGP Single Nucleotide Polymorphism (SNP) Project</b>:<br />[https://www.fruitfly.org/SNP/ Berkeley Drosophila Genome Project, University of California, Berkeley, 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]
 
* <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]
 
* <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]
 
* <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]
 
* <b>Drosophila Genome Nexus</b>: a population genomic resource that provides ''D. melanogaster'' genomes from multiple sources<br />[http://www.johnpool.net/genomes.html University of Wisconsin, Madison, WI, USA]
 
* <b>Drosophila Genome Nexus</b>: a population genomic resource that provides ''D. melanogaster'' genomes from multiple sources<br />[http://www.johnpool.net/genomes.html University of Wisconsin, Madison, WI, USA]
* <b>Drosophila Polymorphism Database</b>:<br />[http://dpdb.uab.es/dpdb/dpdb.asp DPDB, Universitat Autonoma de Barcelona, Barcelona, Spain]
+
* <b>DSPR</b>, Drosophila Synthetic Population Resource:<br />[https://wfitch.bio.uci.edu/~dspr/index.html DSPR, University of Kansas and UC Irvine, USA]
* <b>DPGP</b>, Drosophila Population Genomics Project:<br />[http://www.dpgp.org/ DPGP, University of California, Davis, USA]
+
* <b>Global Diversity Lines</b>: a Five Continent Reference Panel of Sequenced Drosophila melanogaster Strains<br />[https://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?study=SRP050151 Global Diversity Lines, Cornell University, Ithaca, NY, 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]
 
* <b>FlySNP Project</b>:<br />[http://flysnp.imp.univie.ac.at/ FlySNP, Austrian Academy of Sciences, Austria]
 
* <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]
 
* <b>Global Diversity Lines</b>: a Five Continent Reference Panel of Sequenced Drosophila melanogaster Strains<br />[http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?study=SRP050151 Global Diversity Lines, Cornell University, Ithaca, NY, USA]
 
  
=Protein Analysis=
+
=Protein Analysis and Modification=
* <b>ExPASy</b>, the SIB Bioinformatics Resource Portal which provides access to scientific databases and software tools in different areas of life sciences:<br />[http://expasy.org/ SIB Swiss Institute of Bioinformatics, Genève, Switzerland]
+
* <b>AlphaFold Protein Structure Database</b>, AlphaFold DB provides open access to protein structure predictions; An AI system developed by DeepMind that predicts a protein’s 3D structure from its amino acid sequence:<br />[https://alphafold.ebi.ac.uk/ EMBL-EBI, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK]
* <b>GPCRDB</b>, information system for G protein-coupled receptors (GPCRs):<br />[http://www.gpcr.org/7tm/ GPCRDB, The GPCRDB (G Protein-Coupled Receptor Data Base) partnership]
+
* <b>ExPASy</b>, the SIB Bioinformatics Resource Portal which provides access to scientific databases and software tools in different areas of life sciences:<br />[https://www.expasy.org/ SIB Swiss Institute of Bioinformatics, Genève, Switzerland]
 +
* <b>GPCRDB</b>, information system for G protein-coupled receptors (GPCRs):<br />[https://gpcrdb.org/ GPCRDB, The GPCRDB (G Protein-Coupled Receptor Data Base) partnership]
 
* <b>InterPro</b> protein domain analysis of Drosophila:<br />[http://www.ebi.ac.uk/interpro/ InterPro: protein sequence analysis & classification, EBI, UK]
 
* <b>InterPro</b> protein domain analysis of Drosophila:<br />[http://www.ebi.ac.uk/interpro/ InterPro: protein sequence analysis & classification, EBI, UK]
* <b>MEROPS</b>, an information resource for peptidases:<br />[http://merops.sanger.ac.uk/ MEROPS, Wellcome Trust Sanger Institute, Hinxton, UK]
+
* <b>iProteinDB</b> Integrated Protein Database of Post Translational Modifications for Drosophila Genes:<br />[https://www.flyrnai.org/tools/iproteindb/web/ iProteinDB, Harvard Medical School, Boston, MA, USA]
* <b>ModBase</b>, Database of Comparative Protein Structure Models:<br />[http://modbase.compbio.ucsf.edu/modbase-cgi/index.cgi ModBase, UCSF, San Francisco, CA, USA]
+
* <b>MEROPS</b>, an information resource for peptidases:<br />[https://www.ebi.ac.uk/merops/ MEROPS, Wellcome Trust Sanger Institute, Hinxton, UK]
* <b>Panther (Protein Analysis THrough Evolutionary Relationships)</b> protein classification system:<br />[http://panther.appliedbiosystems.com/about.jsp Panther Protein Classification System, Applied Biosystems &amp; Celera, USA]
+
* <b>ModBase</b>, Database of Comparative Protein Structure Models:<br />[https://modbase.compbio.ucsf.edu/modbase-cgi/index.cgi ModBase, UCSF, San Francisco, CA, USA]
* <b>PDB</b>, Protein Data Bank:<br />[http://www.rcsb.org/pdb/home/home.do PDB, The Research Collaboratory for Structural Bioinformatics (RCSB) consortium]
+
* <b>Panther (Protein Analysis THrough Evolutionary Relationships)</b> protein classification system:<br />[https://www.pantherdb.org/ Panther Protein Classification System, Applied Biosystems &amp; Celera, USA]
* <b>PhospoPep</b>, interactive interrogation of MS-derived phosphorylation data from 4 different organisms: <br />[http://www.phosphopep.org/index.php Institute for Systems Biology, Seattle, Washington, USA]
+
* <b>PDB</b>, Protein Data Bank:<br />[https://www.rcsb.org/ PDB, The Research Collaboratory for Structural Bioinformatics (RCSB) consortium]
* <b>ProteinProspector</b>, a proteomics tools for mining sequence databases in conjunction with Mass Spectrometry experiments: <br />[http://prospector.ucsf.edu/prospector/mshome.htm UCSF Mass Spectrometry Facility, San Francisco, California, USA]
+
* <b>PhospoPep</b>, Protein Phosphorylation Database: <br />[http://phosphopep.org/ Institute for Systems Biology, Seattle, Washington, USA]
 +
* <b>ProteinProspector</b>, a proteomics tools for mining sequence databases in conjunction with Mass Spectrometry experiments: <br />[https://prospector.ucsf.edu/prospector/mshome.htm UCSF Mass Spectrometry Facility, San Francisco, California, USA]
 
* <b>RBPDB</b>, the database of RNA-binding protein specificities:<br />[http://rbpdb.ccbr.utoronto.ca/ RBPDB]  
 
* <b>RBPDB</b>, the database of RNA-binding protein specificities:<br />[http://rbpdb.ccbr.utoronto.ca/ RBPDB]  
 
* <b>SMART</b>, 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]
* <b>UniProtKB</b>, 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 />[https://www.uniprot.org/ UniProtKB, The UniProt Consortium]
  
 
=Public Education=
 
=Public Education=
* <b>About the history of Drosophila research</b>, An extensive collection of media pertaining to the history of fruit fly research: <br />[http://www.flyfacility.ls.manchester.ac.uk/forthepublic/outreachresources/#History Manchester Fly Facility, University of Manchester, UK]
+
* <b>About the history of Drosophila research</b>, An extensive collection of media pertaining to the history of fruit fly research: <br />[https://droso4public.wordpress.com/history/ 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]
 
* <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]
 
* <b>''Drosophila'' & Computer Programming Game</b>, A scratch computer game based on the Drosophila life cycle: <br /> [https://poppi62.wordpress.com/2015/08/28/school-flies/#ICT Manchester Fly Facility, University of Manchester, UK]
 
* <b>''Drosophila'' & Computer Programming Game</b>, A scratch computer game based on the Drosophila life cycle: <br /> [https://poppi62.wordpress.com/2015/08/28/school-flies/#ICT Manchester Fly Facility, University of Manchester, UK]
* <b>Genetic Portraits</b>, An overview of commonly used model organisms in genetic research:<br />[http://highered.mheducation.com/sites/007352526x/student_view0/genetic_portrait_chapters_a-e.html McGraw-Hill Higher Education]
+
* <b>Experiments with Drosophila for Biology Courses</b>, An e-resource book for laboratory experiments at under- and post-graduate levels and for research projects in Biology courses :<br />[https://www.ias.ac.in/Publications/e-Books/Experiments_with_Drosophila_for_Biology_Courses Indian Academy of Sciences, India] [http://ftp.flybase.org/flybase/associated_files/Experiments_with_Drosophila_for_Biology_Courses.pdf pdf here ]  
* <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]
 
 
* <b>FlyMove</b>, 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]
* <b>Manchester Fly Facility Public Resource Page</b>:<br />[http://www.flyfacility.ls.manchester.ac.uk/forthepublic/ Manchester Fly Facility, University of Manchester, UK]
+
* <b>Lay articles</b>, A collection of lay articles about fly research: <br />[https://droso4public.wordpress.com/lay-articles/ Manchester Fly Facility, University of Manchester, UK]
 +
* <b>Manchester Fly Facility Public Resource Page</b>:<br />[https://droso4public.wordpress.com/ Manchester Fly Facility, University of Manchester, UK]
  
 
=RNAi=
 
=RNAi=
* <b>DRSC-TRiP-FGR</b>, DRSC/TRiP Functional Genomics Resources:<br />[http://fgr.hms.harvard.edu/ DRSC-TRiP-FGR, Harvard Medical School, Boston, MA, USA]
+
* <b>DRSC-TRiP-FGR</b>, DRSC/TRiP Functional Genomics Resources:<br />[https://fgr.hms.harvard.edu/ DRSC-TRiP-FGR, 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-TRiP-FGR, Harvard Medical School, Boston, MA, USA]
+
* <b>Search by gene(s) to find hit information for genes and DRSC amplicons in DRSC screens</b>:<br /> [https://www.flyrnai.org/RNAi_find_hit_info.html DRSC-TRiP-FGR, Harvard Medical School, Boston, MA, USA]
* <b>FlyRNAi blog</b>, a DRSC resource concerning RNAi, cell-based assays, <i>Drosophila</i> cell culture, high-throughput screening, & fly biology:<br />[http://www.flyrnai.blogspot.com/ flyrnai.blogspot.com]
+
* <b>FlyRNAi blog</b>, a DRSC resource concerning RNAi, cell-based assays, <i>Drosophila</i> cell culture, high-throughput screening, & fly biology:<br />[http://flyrnai.blogspot.com/ flyrnai.blogspot.com]
* <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-TRiP-FGR, Harvard Medical School, Boston, MA, USA]
+
* <b>Fosmid rescue analysis tool</b> for identification of fosmids appropriate for cross-species rescue of RNAi:<br />[https://www.flyrnai.org/cgi-bin/RNAi_find_rescue_compl.pl DRSC-TRiP-FGR, Harvard Medical School, Boston, MA, USA]
 
* <b>GenomeRNAi</b>, Heidelberg, a database of RNA interference (RNAi) screens:<br />[http://www.genomernai.org GenomeRNAi, DKFZ, Heidelberg, Germany]
 
* <b>GenomeRNAi</b>, Heidelberg, a database of RNA interference (RNAi) screens:<br />[http://www.genomernai.org GenomeRNAi, DKFZ, Heidelberg, Germany]
* <b>GESS</b>, off-target RNAi prediction:<br />[http://www.flyrnai.org/gess/ DRSC-TRiP-FGR, Harvard Medical School, Boston, MA, USA]
+
* <b>GESS</b>, off-target RNAi prediction:<br />[https://www.flyrnai.org/gess/ DRSC-TRiP-FGR, 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-TRiP-FGR, Harvard Medical School, Boston, MA, USA]
+
* <b>Predicted Off-Target Free Sequence Regions</b>:<br />[https://www.flyrnai.org/RNAi_find_frag_free.html DRSC-TRiP-FGR, Harvard Medical School, 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]
+
* <b>RNAiCut</b>, Automated Detection of Significant Genes from Functional Genomic Screens:<br /> [https://cb.csail.mit.edu/cb/RNAiCut/ Berger Lab, MIT, Boston, MA, USA]
* <b>RSVP</b>, RNAi Stock Validation & Phenotypes:<br />[http://fgr.hms.harvard.edu/rsvp DRSC-TRiP-FGR, Harvard Medical School, Boston, MA, USA]
+
* <b>RSVP</b>, RNAi Stock Validation & Phenotypes:<br />[https://fgr.hms.harvard.edu/rsvp DRSC-TRiP-FGR, Harvard Medical School, Boston, MA, USA]
* <b>SnapDragon</b>, RNAi Design:<br />[http://www.flyrnai.org/cgi-bin/RNAi_find_primers.pl DRSC-TRiP-FGR, Harvard Medical School, Boston, MA, USA]
+
* <b>SnapDragon</b>, RNAi Design:<br />[https://www.flyrnai.org/cgi-bin/RNAi_find_primers.pl DRSC-TRiP-FGR, Harvard Medical School, Boston, MA, USA]
* <b>TRiP</b>, Transgenic RNAi Project: <br />[http://fgr.hms.harvard.edu/fly-in-vivo-rnai DRSC-TRiP-FGR, Harvard Medical School, Boston, MA, USA]
+
* <b>TRiP</b>, Transgenic RNAi Project: <br />[https://fgr.hms.harvard.edu/fly-in-vivo-rnai DRSC-TRiP-FGR, Harvard Medical School, Boston, MA, USA]
* <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]  
+
* <b>Tsinghua Fly Center</b>, THFC RNAi Stock Collection for triggering RNAi in soma and germline: <br />[https://thfc.zzbd.org/en THFC, Tsinghua Fly Center, Beijing, China]
* <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-TRiP-FGR, Harvard Medical School, Boston, MA, USA]
+
* <b>UP-TORR Fly</b>, a tool for identifying updated targets of RNAi reagents: <br />[https://www.flyrnai.org/up-torr/ Updated Targets of RNAi Reagents, DRSC-TRiP-FGR, Harvard Medical School, Boston, MA, USA]
* <b>VDRC</b>, 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 />[https://shop.vbc.ac.at/vdrc_store/ Genome-wide transgenic Drosophila RNAi libraries, VDRC, Vienna, Austria]
  
 
=Sequence Analysis=
 
=Sequence Analysis=
 
* <b>DCPD</b> -- Drosophila Core Promoter Database, A list of 205 Drosophila melanogaster core promoters aligned by their empirically determined transcription start site: <br />[http://labs.biology.ucsd.edu/Kadonaga/DCPD.htm Kadonaga Lab, UCSD, San Diego, California, USA]
 
* <b>DCPD</b> -- Drosophila Core Promoter Database, A list of 205 Drosophila melanogaster core promoters aligned by their empirically determined transcription start site: <br />[http://labs.biology.ucsd.edu/Kadonaga/DCPD.htm Kadonaga Lab, UCSD, San Diego, California, USA]
* <b>EvoPrinterHD</b>, A "High Definition" view of conserved DNA: <br />[http://evoprinter.ninds.nih.gov/evoprintprogramHD/drosophila.html NINDS, NIH, Bethesda, MD, USA]
+
* <b>FlyPrimerBank</b>, a comprehensive qPCR primer database for Drosophila: <br />[https://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]
+
* <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]
* <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]
+
* <b>Gemme</b>, A fast, scalable and simple method to predict mutational landscapes from natural sequences: <br />[http://www.lcqb.upmc.fr/GEMME/Home.html Gemme, Sorbonne University, Paris, France]
 
* <b>GenePalette</b>, 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]
* <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]
+
* <b>Genie Gene finder for Drosophila: </b>:<br />[https://www.fruitfly.org/seq_tools/genie.html Genie, Berkeley Drosophila Genome Project, University of California, Berkeley, USA]
* <b>HRMA</b> -- 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 /> [https://fgr.hms.harvard.edu/hrma HRMA, DRSC, Harvard Medical School, Boston, MA, USA]
* <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]
+
* <b>MEME Suite</b> -- Motif-based Sequence Analysis Tools: <br />[http://meme-suite.org/ MEME, U. of Queensland, U. of Washington, USA, UCSD, SDSC, NBCR, CBRC, and National Center for Research Resources]
* <b>RepeatMasker</b>: <br />[http://www.repeatmasker.org/ RepeatMasker Institute for Systems Biology, Seattle, WA, USA]
+
* <b>RepeatMasker</b>: <br />[https://www.repeatmasker.org/ RepeatMasker Institute for Systems Biology, Seattle, WA, 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]
+
* <b>Splice Site Prediction for Drosophila</b>:<br />[https://www.fruitfly.org/seq_tools/splice.html Splice Site Prediction, Berkeley Drosophila Genome Project, University of California, Berkeley, USA]
 
* <b>Web Apollo</b>, 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]
 +
 +
=Single Cell RNA-seq=
 +
* <b>ASAP</b> Automated Single-cell Analysis Pipeline: <br />[https://asap.epfl.ch/ ASAP, EPFL, Lausanne, Switzerland, Swiss Institute of Bioinformatics, Lausanne, Switzerland]
 +
 +
* <b>cisTopic</b> Probabilistic modelling of cis-regulatory topics from single cell epigenomics data: <br />[https://github.com/aertslab/cisTopic/ cisTopic, VIB Center for Brain & Disease Research, Leuven, Belgium, Department of Human Genetics, KU Leuven, Leuven, Belgium]
 +
 +
* <b>DeepCMC</b> A Neural Networks (NN) based approach for identifying genes that contain spatial information: <br />[https://github.com/TJU-CMC-Org/SingleCell-DREAM DeepCMC, Thomas Jefferson University, Philadelphia, PA, USA]
 +
 +
* <b>Distmap</b> To spatially map single cell RNA sequencing data by using an existing reference database of in situs: <br />[https://github.com/rajewsky-lab/distmap Distmap, BIMSB and MDC, Berlin, Germany]
 +
 +
* <b>DRscDB</b> DRSC scRNA-seq DataBase: <br />[https://www.flyrnai.org/tools/single_cell/ DRscDB, DRSC, Harvard Medical School, Boston, USA]
 +
 +
* <b>DVEX</b> Drosophila Virtual Expression eXplorer: <br />[https://shiny.mdc-berlin.de/DVEX/ DVEX, BIMSB and MDC, Berlin, Germany]
 +
 +
* <b>Fly Cell Atlas</b> A consortium of Drosophila researchers interested in single-cell genomics, transcriptomics, and epigenomics: <br />[https://flycellatlas.org/ Fly Cell Atlas, Founders - Stein Aerts, Leuven, Belgium, Bart Deplancke, Lausanne, Switzerland, Robert Zinzen, Berlin, Germany]
 +
 +
* <b>Lasso.TopX</b> An approach using the Lasso and ranking statistics for identifying genes that contain spatial information: <br />[https://github.com/TJU-CMC-Org/SingleCell-DREAM/ Lasso.TopX, Thomas Jefferson University, Philadelphia, PA, USA]
 +
 +
* <b>novoSpaRc</b> Predicts locations of single cells in space by solely using single-cell RNA sequencing data.: <br />[https://github.com/rajewsky-lab/novosparc novoSpaRc, Harvard and Broad Institute, Cambridge, MA, USA, Max Delbrück Center, Berlin, Germany]
 +
 +
* <b>SCEA</b> Single Cell Expression Atlas - Single Cell Gene Expression Across Species: <br />[https://www.ebi.ac.uk/gxa/sc SCEA, EMBL-EBI, Hinxton, UK, Sanger Institute, Wellcome Genome Campus, Hinxton, UK, Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK]
 +
 +
* <b>SCENIC</b> Single-Cell Regulatory Network Inference and Clustering <br />[https://github.com/aertslab/SCENIC SCENIC, Center for Brain & Disease Research, Leuven, Belgium, KU Leuven, Leuven, Belgium, University of Liege, Liege, Belgium, VIB Center for Cancer Biology, Leuven, Belgium]
 +
 +
* <b>SCope</b> Fast Visualization Tool for Large-Scale and High Dimensional Single-Cell Data <br />[https://github.com/aertslab/SCope SCope, VIB KU Leuven, Leuven, Belgium]
 +
 +
* <b>Seurat</b> An R package designed for QC, analysis, and exploration of single-cell RNA-seq data.: <br />[https://satijalab.org/seurat/ Seurat, NYU, NY, NY, USA]
 +
 +
* <b>VSN</b> A Repository of Pipelines for Single-Cell Data Analysis in Nextflow DSL2:  <br />[https://github.com/vib-singlecell-nf/vsn-pipelines VSN-Pipelines]
  
 
=Taxonomy=
 
=Taxonomy=
* <b>Drosophilidae Taxonomic Database</b>:<br />[http://bioinfo.lowtem.hokudai.ac.jp/db/modules/stdb/ Drosophilidae Taxonomic Database, 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]
 
 
* <b>FlyPhenomics</b>, 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]
 +
* <b>TaxoDros</b> Drosophilidae Taxonomic Database:<br />[https://bioinfo.museum.hokudai.ac.jp/ Drosophilidae Taxonomic Database, Japan]
 
* <b>TaxoDros</b>, 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]
* <b>Taxonomy</b>, NCBI Taxonomy Database:<br />[http://www.ncbi.nlm.nih.gov/taxonomy NCBI, Bethesda, MD USA]
+
* <b>Taxonomy</b>, NCBI Taxonomy Database:<br />[https://www.ncbi.nlm.nih.gov/taxonomy NCBI, Bethesda, MD USA]
 +
* <b>Taxonomy of Drosophilidae - JDD - Japan Drosophila Database</b> <br />[http://www.drosophila.jp/jdd/index_en.html Japan Drosophila Database (JDD) on Taxonomy, Japan]
  
 
=Transcription Regulation Databases and Tools=
 
=Transcription Regulation Databases and Tools=
* <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]
+
* <b>CIS-BP</b>, The online library of transcription factors and their DNA binding motifs:<br />[http://cisbp.ccbr.utoronto.ca/ CIS-BP, Hughes Lab, University of Toronto, Toronto, Canada and Weirauch lab, Cincinnati Children's Hospital, Cincinnati, OH, USA]
* <b>cis-analyst</b>, Searching the Drosophila genome for clusters of binding sites: <br />[http://rana.lbl.gov/cis-analyst/ cis-analyst, Berkeley, USA]
+
* <b>EPD</b>, the Eukaryotic Promoter Database:<br />[https://epd.expasy.org/epd EPD, Epalinges s/Lausanne, Switzerland]
* <b>CORE</b>, A database utilizing the ElemeNT algorithm (see below) to annotate individual Drosophila observed TSS (using either CAGE or RNAseq data) for the presence of the various core promoter elements: <br />[http://lifefaculty.biu.ac.il/gershon-tamar/index.php/core-description Juven-Gershon Lab, Bar-Ilan University, Ramat-Gan, Israel]
+
* <b>Fly Factor Survey</b> - Database of Drosophila TF DNA-binding Specificities: <br />[http://pgfe.umassmed.edu/ffs/ FLy Factor Survey, UMass Medical School, Worcester, MA, USA]
* <b>DBD</b>, Transcription factor prediction database: <br />[http://www.transcriptionfactor.org/index.cgi?Home DBD, MRC, Cambridge, UK]
+
* <b>FlyReg</b>, DNase I Footprint Database - retired<br />[http://www.flyreg.org/ University of Manchester Bioinformatics Resources, University of Manchester, UK]
* <b>ElemeNT</b>, An interactive tool for rapid and convenient detection of core promoter elements within a given sequence, implemented in Perl programming language: <br />[http://lifefaculty.biu.ac.il/gershon-tamar/index.php/element-description Juven-Gershon Lab, Bar-Ilan University, Ramat-Gan, Israel]
+
* <b>JASPAR</b>, A database of transcription factor (TF) binding profiles stored as position frequency matrices and TF flexible models for TFs across multiple species.<br />[https://jaspar.elixir.no/ JASPAR]
 
+
* <b>Neural Network Promoter Prediction for Drosophila</b>:<br />[https://www.fruitfly.org/seq_tools/promoter.html Neural Network Promoter Prediction, Berkeley Drosophila Genome Project, University of California, Berkeley, CA, USA]
* <b>EPD</b>, the Eukaryotic Promoter Database:<br />[http://epd.vital-it.ch/drosophila/drosophila_database.php/ EPD, Epalinges s/Lausanne, Switzerland]
+
* <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, NY, USA]
* <b>Fly Factor Survey</b> - Database of Drosophila TF DNA-binding Specificitiies: <br />[http://pgfe.umassmed.edu/ffs/ FLy Factor Survey, UMass Medical School, Worcester, MA, USA]
+
* <b>REDfly</b>, Regulatory Element Database for Drosophila:<br />[http://redfly.ccr.buffalo.edu/ REDfly, University at Buffalo, New York, Buffalo, NY, USA]
* <b>FlyReg</b>, DNase I Footprint Database:<br />[http://www.flyreg.org/ University of Manchester Bioinformatics Resources, University of Manchester, UK]
+
* <b>ReMap</b>, a large-scale integrative analysis of DNA-binding experiments for Homo sapiens, Mus musculus, Dropshiphila melanogaster, and Arabadopsis thaliana transcriptional regulators based on manual curation of ChIP-seq, ChIP-exo, DAP-seq from public sources:<br />[https://remap.univ-amu.fr/ ReMap, TAGC Inserm, Marseille, France]
* <b>i-cisTarget</b>, An integrative genomics method for the prediction of regulatory features and cis-regulatory modules in Human, Mouse, and Fly:<br />[http://gbiomed.kuleuven.be/apps/lcb/i-cisTarget/ i-cisTarget, University of Leuven, Leuven, Belgium]
+
* <b>FlyTF.org</b>, The Drosophila Transcription Factor Database:<br />[https://www.mrc-lmb.cam.ac.uk/genomes/FlyTF/old_index.html FlyTF.org, MRC Cambridge, UK]
* <b>Neural Network Promoter Prediction for Drosophila</b>:<br />[http://www.fruitfly.org/seq_tools/promoter.html Neural Network Promoter Prediction, Berkeley Drosophila Genome Project, University of California, Berkeley, USA]
+
* <b>scEnhancer</b>, A database of single cell enhancer annotation in human, mouse, and fly:<br />[http://enhanceratlas.net/scenhancer/ scEnhancer, Sun Yat-sen University, Shenzhen, China and Johns Hopkins University, Baltimore, MD, USA]
* <b>OnTheFly</b>, Database of Drosophila Transcription Factors and Transcription Factor Binding Sites <br />[https://bhapp.c2b2.columbia.edu/OnTheFly/index.php OnTheFly, Columbia University, USA]
+
* <b>TRANSFAC</b>, A database of transcription factors and their binding sites:<br />[http://gene-regulation.com/pub/databases.html#transfac TRANSFAC, Braunschweig, Germany]
* <b>PREdictor</b>, to identify Polycomb/Trithorax response elements: <br />[http://bibiserv.techfak.uni-bielefeld.de/predictor/ PREdictor, Bielefeld University, Germany]
+
* <b>UniPROBE</b>, Universal PBM (protein binding microarray) Resource for Oligonucleotide Binding Evaluation:<br />[http://thebrain.bwh.harvard.edu/uniprobe/ UniPROBE, Bulyk lab, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA]
* <b>REDfly</b>, Regulatory Element Database for Drosophila:<br />[http://redfly.ccr.buffalo.edu/ REDfly, University at Buffalo, New York, USA]
 
* <b>The Drosophila Transcription Factor Database</b>:<br />[http://www.flytf.org/ FlyTF.org, MRC Cambridge, UK]
 
* <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=
*Please [http://flybase.org/cgi-bin/mailto-fbhelp.html contact Flybase] to suggest a tool or resource for the list.
+
*Please [http://flybase.org/contact/email contact Flybase] to suggest a tool or resource for the list.
  
 
[[Category:DONE]]
 
[[Category:DONE]]

Latest revision as of 13:33, 19 March 2024

Atlases, Images and Videos

Cell Lines and Cell Culture

CRISPRs and TALENs

Data Repositories

DNA Reagents

Drosophila Genomes Data and Metadata

Gene Expression Databases and Tools

Gene Groups

General Bioinformatics Tools

Gene Set Enrichment Analysis

A summary table of selected GSEA tools with information about set up can be found here

Genome Sequencing Projects

Human Disease: Drosophila Models and Orthologous Genes

Interaction and Pathway Databases

Metabolomics

Miscellaneous

Non-coding (ncRNA) Databases and Tools

General

lncRNA

miRNA

General

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.
  • miRNEST, An integrated collection of miRNA predictions from high-throughput sequencing experiments and external database annotations (last updated 2015):
    miRNEST, The Adam Mickiewicz University in Poznan, Poznan, Poland
  • TransmiR, A database of transcription factor-microRNA regulation (last updated 2018):
    TransmiR, Peking University Health Science Center, Peking, Chin

miRNA Target Prediction

Validated miRNA Targets

Comparative miRNA Analysis

rRNA

tRNA

snoRNA

SRP RNA

Ontology Resources

Orthology Predictions

Phylogenetic Comparison Tools

Population Biology and Polymorphism Resources

Protein Analysis and Modification

Public Education

RNAi

Sequence Analysis

Single Cell RNA-seq

  • VSN A Repository of Pipelines for Single-Cell Data Analysis in Nextflow DSL2:
    VSN-Pipelines

Taxonomy

Transcription Regulation Databases and Tools

Suggest a tool or resource