Difference between revisions of "FlyBase:Drosophila Online Resources"

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* <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>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 />[https://www.jove.com/search? Jove, Journal of Visualized Experiments, 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>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>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>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>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]
  
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* <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 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://crisprflydesign.org/ Bullolk Lab, MRC Laboratory of Molecular Biology, Cambridge, UK]
* <b>CRISPResso2 </b> CRISPR Design Tool:<br />[https://crispresso.pinellolab.partners.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>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>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>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]
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* <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>, Overview: <br />[https://flycrispr.org/ 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>, Target Finder:<br />[https://flycrispr.org/target-finder// 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>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]
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=Data Repositories=
 
=Data Repositories=
 
* <b>Array Express</b> - Functional Genomics Data:<br />[https://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 />[https://www.ddbj.nig.ac.jp/index-e.html 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 />[https://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 />[https://www.ebi.ac.uk/ena/browser/home 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>ENCODE</b>, Encyclopedia of DNA Elements (including modENCODE and modERN):<br />[https://www.encodeproject.org/ ENCODE, Stanford University, Stanford, USA]
 
* <b>ENCODE</b>, Encyclopedia of DNA Elements (including modENCODE and modERN):<br />[https://www.encodeproject.org/ ENCODE, Stanford University, Stanford, USA]
* <b>Ensembl Genome Browser</b>:<br />[http://useast.ensembl.org/index.html EMBL-EBI, Hinxton, UK]
 
 
* <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>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 />[https://www.ncbi.nlm.nih.gov/Genbank/ GenBank, NCBI, Bethesda, 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 />[https://www.ncbi.nlm.nih.gov/geo/info/datasets.html NCBI, Bethesda, USA]
 
* <b>GEO Datasets</b>, Gene Expression Omnibus:<br />[https://www.ncbi.nlm.nih.gov/geo/info/datasets.html NCBI, Bethesda, USA]
 
* <b>modERN</b>, model organism Encyclopedia of Regulatory Networks:<br />[http://epic.gs.washington.edu/modERN/ modERN, University of Washington, Seattle, 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</b>, National Center for Biotechnology Information:<br />[http://www.ncbi.nlm.nih.gov Bethesda, MD USA]
 
* <b>NCBI</b>, National Center for Biotechnology Information:<br />[http://www.ncbi.nlm.nih.gov 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>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</b>, Biomedical literature full-text archive:<br />[https://www.ncbi.nlm.nih.gov/pubmed PubMed, NCBI, Bethesda, USA]
+
* <b>PubMed</b>, Biomedical literature full-text archive:<br />[https://pubmed.ncbi.nlm.nih.gov/ PubMed, NCBI, Bethesda, USA]
 
* <b>PubMed Central</b>, Biomedical literature citations and abstracts:<br />[https://www.ncbi.nlm.nih.gov/pmc/ PubMed Central, NCBI, Bethesda, USA]
 
* <b>PubMed Central</b>, Biomedical literature citations and abstracts:<br />[https://www.ncbi.nlm.nih.gov/pmc/ PubMed Central, NCBI, Bethesda, USA]
 
* <b>SRA</b>, Sequence Read Archive:<br />[https://www.ncbi.nlm.nih.gov/sra SRA, NCBI, Bethesda, MD, USA]
 
* <b>SRA</b>, Sequence Read Archive:<br />[https://www.ncbi.nlm.nih.gov/sra SRA, NCBI, Bethesda, MD, USA]
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=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>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 />[https://www.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>DIGITtally</b>, Finding Genes of Interest DIGITtally: <br /> [https://www.digittally.org/ DIGITtally, University of Glasgow, Glasgow, UK]
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* <b>FlyGut-seq</b>, a transcriptomic resource that complements the original [http://flygut.epfl.ch/ Flygut website]:<br />[http://flygutseq.buchonlab.com/ Buchon Lab, Cornell University, Ithaca, NY, USA]
 
* <b>FlyGut-seq</b>, a transcriptomic resource that complements the original [http://flygut.epfl.ch/ Flygut website]:<br />[http://flygutseq.buchonlab.com/ Buchon Lab, Cornell University, Ithaca, NY, USA]
 
* <b>FlyLight</b>, Expression Patterns of GAL4, 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>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 />[https://www.fly-trap.org/ flytrap, University of Edinburgh, UK]
* <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>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>GEO Profiles</b>, Gene Expression Omnibus:<br />[http://www.ncbi.nlm.nih.gov/geo/info/profiles.html GEO, NCBI, Bethesda, MD USA]
+
* <b>GEO Profiles</b>, Gene Expression Omnibus:<br />[https://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>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>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 />[https://calla.rnet.missouri.edu/rnaminer/ Cheng Lab, University of Missouri, Mizzou, Columbia, MO, USA]
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=General Bioinformatics Tools=
 
=General Bioinformatics Tools=
* <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>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>ApE</b>, A plasmid Editor:<br />[https://jorgensen.biology.utah.edu/wayned/ape/ ApE, University of Utah, Salt Lake City, UT, USA]
 
* <b>ApE</b>, A plasmid Editor:<br />[https://jorgensen.biology.utah.edu/wayned/ape/ ApE, University of Utah, Salt Lake City, UT, USA]
 
* <b>Bioconductor</b>, Open Source Software for Bioinformatics:<br />[https://www.bioconductor.org/ Fred Hutchinson Cancer Research Center, Seattle, USA]
 
* <b>Bioconductor</b>, Open Source Software for Bioinformatics:<br />[https://www.bioconductor.org/ Fred Hutchinson Cancer Research Center, Seattle, USA]
* <b>BioMart</b>, Data Warehouse:<br />[http://useast.ensembl.org/info/data/biomart/index.html BioMart, EMBL-EBI, OICR, SRSI]
 
 
* <b>Bioz</b>, Insights and recommendations for products, equipment and assays:<br />[https://www.bioz.com/search/Drosophila Palo Alto, CA, USA]
 
* <b>Bioz</b>, Insights and recommendations for products, equipment and assays:<br />[https://www.bioz.com/search/Drosophila Palo Alto, CA, USA]
 
* <b>Cytoscape</b> -- Network Data Integration, Analysis, and Visualization in a Box:<br />[https://cytoscape.org/ Cytoscape, Cytoscape Consortium, Canada, France, and USA]
 
* <b>Cytoscape</b> -- Network Data Integration, Analysis, and Visualization in a Box:<br />[https://cytoscape.org/ Cytoscape, Cytoscape Consortium, Canada, France, and USA]
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A summary table of selected GSEA tools with information about set up can be found [[FlyBase:GSEA|<b>here</b>]]
 
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>DAVID</b>, Database for Annotation, Visualization and Integrated Discovery :<br />[https://david.ncifcrf.gov/ DAVID, Laboratory of Human Retrovirology and Immunoinformatics, Frederick, MD, USA]]
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* <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>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>GOC</b>, GO Enrichment Analysis:<br />[https://geneontology.org/ Gene Ontology Consortium]
* <b>GSEA</b>, Gene Set Enrichment Analysis:<br />[http://www.broadinstitute.org/gsea/index.jsp GSEA, Broad Institute, Cambridge, MA, USA]
+
* <b>GSEA</b>, Gene Set Enrichment Analysis:<br />[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>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>GOrilla</b>, Gene Ontology enRIchment anaLysis and visuaLizAtion tool:<br />[https://cbl-gorilla.cs.technion.ac.il/ GOrilla, Technion, Israel Institute of Technology, Israel]
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=Interaction and Pathway Databases=
 
=Interaction and Pathway Databases=
* <b>BioCyc - FLY</b> -- Curated Drosophila melanogaster Pathways:<br />[http://biocyc.org/FLY/organism-summary?object=FLY FlyCyc, Harvard University, Cambridge, USA]
+
* <b>BioCyc - FLY</b> -- Curated Drosophila melanogaster Pathways:<br />[https://biocyc.org/FLY/organism-summary?object=FLY FlyCyc, Harvard University, Cambridge, USA]
 
* <b>BioGRID</b>, The General Repository for Interaction Datasets:<br />[https://thebiogrid.org/index.php BioGRID, Mount Sinai Hospital, Toronto, Canada]
 
* <b>BioGRID</b>, The General Repository for Interaction Datasets:<br />[https://thebiogrid.org/index.php BioGRID, Mount Sinai Hospital, Toronto, Canada]
 
* <b>COMPLEAT</b>, protein COMPLex Enrichment Analysis Tool:<br />[https://www.flyrnai.org/compleat/ COMPLEAT, DRSC, Harvard Medical School, Boston, MA, USA]
 
* <b>COMPLEAT</b>, protein COMPLex Enrichment Analysis Tool:<br />[https://www.flyrnai.org/compleat/ COMPLEAT, DRSC, Harvard Medical School, Boston, MA, USA]
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* <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>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 />[https://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>MIST</b> -- Molecular Interactions Search Tool:<br />[https://fgrtools.hms.harvard.edu/MIST/ MIST, Harvard Medical School, Boston, MA, USA]
 
* <b>MIST</b> -- Molecular Interactions Search Tool:<br />[https://fgrtools.hms.harvard.edu/MIST/ MIST, Harvard Medical School, Boston, MA, USA]
 
* <b>Reactome Pathway Database</b>:<br />[https://reactome.org/ Reactome, OICR, Ontario, Canada, EMBL-EBI, UK, NYU Medical Center, NY, USA]
 
* <b>Reactome Pathway Database</b>:<br />[https://reactome.org/ Reactome, OICR, Ontario, Canada, EMBL-EBI, UK, NYU Medical Center, NY, USA]
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* <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>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>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>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>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>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>FlyTree</b>, the Drosophila Researcher Genealogy has been incorporated into the Academic Tree Project: <br />[https://academictree.org/flytree/ FlyTree, USA]
 
* <b>FlyTree</b>, the Drosophila Researcher Genealogy has been incorporated into the Academic Tree Project: <br />[https://academictree.org/flytree/ FlyTree, USA]
* <b>GenAge</b> -- The Ageing Gene Database:<br />[http://genomics.senescence.info/genes/ Human Ageing Genomic Resources, Institute of Integrative Biology, Liverpool, UK]
+
* <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>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>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>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>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>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>Interactive Fly</b>, A cyberspace guide to Drosophila development and metazoan evolution<br />[http://www.sdbonline.org/fly/aimain/1aahome.htm Interactive Fly, Bethesda, MD, USA]
+
* <b>Interactive Fly</b>, A cyberspace guide to Drosophila development and metazoan evolution<br />[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>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]
Line 232: Line 229:
 
* <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>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>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>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>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 />[http://rnacentral.org/ RNAcentral, EMBL-EBI, Hinxton, UK]
+
* <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]
  
 
==lncRNA==
 
==lncRNA==
Line 239: Line 236:
 
==miRNA==
 
==miRNA==
 
===General===
 
===General===
* <b>miRBase</b>, A searchable database of published miRNA sequences and annotations (current miBase release is 22 - last updated 2018):<br />[http://www.mirbase.org/ miRBase, University of Manchester, UK]<br />
+
* <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>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>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]
Line 246: Line 243:
 
===miRNA Target Prediction===
 
===miRNA Target Prediction===
 
* <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>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 />[http://www.flyrnai.org/cgi-bin/DRSC_MinoTar.pl MinoTar, DRSC, Harvard Medical School, Boston, MA, USA]
+
* <b>MinoTar</b>, Predict microRNA Targets in Coding Sequence (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]
 
* <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]
  
Line 274: Line 271:
 
* <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.org/ 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>OLS - 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 />[https://protege.stanford.edu/ 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>Gene2Function</b>:<br /> [https://www.gene2function.org/search/ Gene2Function, Harvard Medical School, Boston, MA, USA]
 
* <b>Gene2Function</b>:<br /> [https://www.gene2function.org/search/ Gene2Function, Harvard Medical School, Boston, MA, USA]
 
* <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>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>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>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>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/homologene NCBI, Bethesda, MD, USA]
+
* <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>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>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>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>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>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 />[http://omabrowser.org/oma/home/ Nucl. Acids Res. 43 (D1): D240-D249. doi: 10.1093/nar/gku1158]
+
* <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>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>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/orthoinspectorv3/ ICube Laboratory, Graffenstaden, France]
+
* <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>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]
Line 302: Line 299:
  
 
=Phylogenetic Comparison Tools=
 
=Phylogenetic Comparison Tools=
* <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>HomoloGene</b> -- automated system fo constructing putative homology groups:<br />[http://www.ncbi.nlm.nih.gov/homologene NCBI, Bethesda, 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>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>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>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>MANTiS</b>, a phylogenetic framework for multi-species genome comparisons:<br />[https://www.mantisdb.org/MANTiS/Welcome.html MANTiS, Université Libre de Bruxelles, Belgium]
Line 310: Line 307:
  
 
=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]
Line 319: Line 316:
 
=Protein Analysis and Modification=
 
=Protein Analysis and Modification=
 
* <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>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>ExPASy</b>, the SIB Bioinformatics Resource Portal which provides access to scientific databases and software tools in different areas of life sciences:<br />[http://expasy.org/ SIB Swiss Institute of Bioinformatics, Genève, Switzerland]
+
* <b>ExPASy</b>, the SIB Bioinformatics Resource Portal which provides access to scientific databases and software tools in different areas of life sciences:<br />[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>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>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>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>MEROPS</b>, an information resource for peptidases:<br />[https://ebi.ac.uk/merops/ MEROPS, Wellcome Trust Sanger Institute, Hinxton, UK]
+
* <b>MEROPS</b>, an information resource for peptidases:<br />[https://www.ebi.ac.uk/merops/ MEROPS, Wellcome Trust Sanger Institute, Hinxton, UK]
 
* <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>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>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>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>PDB</b>, Protein Data Bank:<br />[https://www.rcsb.org/ PDB, The Research Collaboratory for Structural Bioinformatics (RCSB) consortium]
 
* <b>PDB</b>, Protein Data Bank:<br />[https://www.rcsb.org/ PDB, The Research Collaboratory for Structural Bioinformatics (RCSB) consortium]
 
* <b>PhospoPep</b>, Protein Phosphorylation Database: <br />[http://phosphopep.org/ Institute for Systems Biology, Seattle, Washington, 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 />[http://prospector.ucsf.edu/prospector/mshome.htm UCSF Mass Spectrometry Facility, San Francisco, California, 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]
Line 345: Line 342:
 
* <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>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 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>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 />[https://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 />[https://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 />[https://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 />[https://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 />[https://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]

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