Difference between revisions of "FlyBase:Drosophila Online Resources"

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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>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]
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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 />[https://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]
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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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=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>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>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>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>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>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 />[http://www.flyrnai.org/cgi-bin/DRSC_gene_lookup.pl Gene Lookup, DRSC, Harvard Medical School, Boston, MA, USA]
+
* <b>Gene Lookup</b>, Gene and Reagent Lookup:<br />[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]
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* <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 />[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 />[https://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]
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=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]
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* <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]
Line 350: Line 347:
 
* <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