Difference between revisions of "FlyBase:Drosophila Online Resources"

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=Comparative Analyses and Genome Databases=
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=Atlases, Images and Videos=
* Assembly/Alignment/Annotation of 12 related Drosophila species:<br />[http://rana.lbl.gov/drosophila/ Assembly/Alignment/Annotation, LBNL, USA]
+
* <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]
* BDGP Single Nucleotide Polymorphism (SNP) Project:<br />[http://www.fruitfly.org/SNP/ Berkeley Drosophila Genome Project, University of California, Berkeley, USA]
+
* <b>CSIRO</b> Anatomical Atlas of Flies:<br />[http://www.ento.csiro.au/biology/fly/fly.html# CSIRO Entomology, Australia]
* Berkeley Drosophila Genome Project (BDGP):<br />[http://www.fruitfly.org/ BDGP, 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]
* BDTNP, ChIP/chip in vivo DNA binding data:<br />[http://bdtnp.lbl.gov/Fly-Net/chipchip.jsp?w=summary Berkeley Drosophila Transcription Network Project, University of California, Berkeley, USA]
+
* <b>FlyCircuit</b>, a Database of Drosophila Brain Neurons:<br />[http://www.flycircuit.tw/ FlyCircuit, National Tsing Hua University, Taiwan]
* CluSTr protein sequence similarity analysis of Drosophila:<br />[http://www.ebi.ac.uk/integr8/ClustrAnalysisPage.do?orgProteomeID=17 CluSTr proteome analysis, EBI, UK]
+
* <b>FlyMove</b>, an Image, Movie and Interactive Shockwave Resource:<br />[http://flymove.uni-muenster.de/ FlyMove, Muenster, Germany]
* ''D. pseudoobscura'' genome project:<br />[https://www.hgsc.bcm.edu/arthropods/drosophila-pseudoobscura-genome-project pseudoobscura Human Genome Sequencing Center, Baylor College of Medicine, 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]
* ''D. simulans'' genome project:<br />[http://genome.wustl.edu/genomes/detail/drosophila-simulans-white-501/ simulans White 501 Genome Sequencing Center, Washington University, USA]
+
* <b>FlyView</b>, a Drosophila Image Database:<br />[http://flyview.uni-muenster.de/ FlyView, Muenster, Germany]
* ''D. yakuba'' genome project:<br />[http://genome.wustl.edu/genomes/detail/drosophila-yakuba/ yakuba Genome Sequencing Center, Washington University, USA]
+
* <b>GETDB</b>, a Gal4 enhancer trap database:<br />[https://kyotofly.kit.jp/stocks/GETDB/getdb.html GETDB, Kyoto Institute of Technology, Kyoto, Japan]
* ''D. melanogaster'' UCSC Genome Browser Gateway:<br />[http://genome.ucsc.edu/cgi-bin/hgGateway?hgsid=392011865_gtu3Ax0AafEkl925NpQE4ZH8Py7I&clade=insect&org=0&db=0 melanogaster, UCSC Genome Browser, University of California, Santa Cruz, USA]
+
* <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]
* DDBJ, the DNA Data Bank of Japan:<br />[http://www.ddbj.nig.ac.jp/ DDBJ, National Institute of Genetics, Mishima, Japan]
+
* <b>Jove</b>, videos of experimental techniques:<br />[http://www.jove.com/index/browse.stp?Search=Drosophila Jove, Journal of Visualized Experiments, USA]
* DNase I Footprint Database<nowiki>: </nowiki><br />[http://www.flyreg.org/ University of Manchester Bioinformatics Resources, University of Manchester, 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]
* ''Drosophila melanogaster'' Exon Database (DEDB):<br />[http://proline.bic.nus.edu.sg/dedb/ DEDB, National University of Singapore]
+
* <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]
* Drosophila Polymorphism Database:<br />[http://bioinformatica.uab.es/dpdb/ Drosophila Polymorphism Database, Univ. Autònoma de Barcelona, Spain]
 
* Drosophila Population Genomic Project (DPGP):<br />[http://www.dpgp.org/ DPGP, University of California, Davis, USA]
 
* Drosophila simulans and yakuba sequencing projects:<br />[http://www.dpgp.org/sim_yak/index.html DPGP, University of California, Davis, USA]
 
* Drosophilidae Taxonomic Database:<br />[http://bioinfo.lowtem.hokudai.ac.jp/db/modules/stdb/ Drosophilidae Taxonomic Database, Japan]
 
* Drosophilidae Taxonomy - Collection of Papers:<br />[http://www.dgrc.kit.ac.jp/~jdd/class/index.html Japan Drosophila Database (JDD) on Taxonomy, Japan]
 
* DRSC, Drosophila RNAi Screening Center:<br />[http://www.flyrnai.org/index.html DRSC, Harvard Medical School, Boston, MA, USA]
 
* ENA, European Nucleotide Archive:<br />[http://www.ebi.ac.uk/embl/ ENA, European Nucleotide Archive, EMBL-EBI, Cambridge, UK]
 
* EPD, the Eukaryotic Promoter Database:<br />[http://www.epd.isb-sib.ch/ EPD, Epalinges s/Lausanne, Switzerland]
 
* euGenes, Genomic Information for Eukaryotic Organisms, including Drosophila:<br />[http://iubio.bio.indiana.edu/eugenes/  euGenes, Indiana University, USA]
 
* EvoPrinter, Identification of Evolutionarily Resilient DNA Sequences<br />[http://evoprinter.ninds.nih.gov/ NINDS, NIH, Bethesda MD, USA]
 
* FlyAtlas, the Drosophila adult gene expression atlas:<br />[http://www.flyatlas.org/ FlyAtlas, University of Glasgow, UK]
 
* FlyMine, an integrated database for Drosophila &amp; Anopheles genomics:<br />[http://www.flymine.org/ University of Cambridge, United Kingdom]
 
* FlyPhenomics, phenotypic differences between species of the ''D. melanogaster'' subgroup:<br />[http://www.normalesup.org/~vorgogoz/FlyPhenomics/ FlyPhenomics, Paris, France]
 
* FlySNP Project:<br />[http://flysnp.imp.univie.ac.at/ FlySNP, Austrian Academy of Sciences, Austria]
 
* GenBank,the NIH genetic sequence database:<br />[http://www.ncbi.nlm.nih.gov/Genbank/ GenBank, NCBI, Bethesda, MD USA]
 
* GenomeRNAi, Heidelberg, a database of RNA interference (RNAi) screens in cultured Drosophila cells:<br />[http://www.dkfz.de/signaling2/rnai/index.php GenomeRNAi, DKFZ, Heidelberg, Germany]
 
* GEO, NCBI's Gene Expression Omnibus:<br />[http://www.ncbi.nlm.nih.gov/geo/ GEO, NCBI, Bethesda, MD USA]
 
* GPCRDB, information system for G protein-coupled receptors (GPCRs):<br />[http://www.gpcr.org/7tm/ GPCRDB, The GPCRDB (G Protein-Coupled Receptor Data Base) partnership]
 
* Homophila, Human Disease to Drosophila Gene Database:<br />[http://superfly.ucsd.edu/homophila/  Homophila, San Diego, USA]
 
* InParanoid, Eukaryotic Ortholog Groups:<br />[http://inparanoid.sbc.su.se/cgi-bin/index.cgi InParanoid, Karolinska Institute, Sweden]
 
* InterPro protein domain analysis of Drosophila:<br />[http://www.ebi.ac.uk/interpro/ InterPro: protein sequence analysis & classification, EBI, UK]
 
* MANTiS a phylogenetic framework for multi-species genome comparisons:<br />[http://www.mantisdb.org/MANTiS/Welcome.html MANTiS, Université Libre de Bruxelles, Belgium]
 
* MEROPS, an information resource for peptidases:<br />[http://merops.sanger.ac.uk/ MEROPS, The Sanger Institute, Cambridge, UK]
 
* miRBase, microRNA data:<br />[http://microrna.sanger.ac.uk/sequences/index.shtml miRBase, The Sanger Institute, Cambridge, UK]
 
* MitoDrome, ''Drosophila melanogaster'' nuclear genes encoding for mitochondrial proteins:<br />[http://mitodrome.ba.itb.cnr.it/ MitoDrome, Bari, Italy]
 
* Mitotic Spindle Assembly Database:<br />[http://rnai.ucsf.edu/mitospindlescreen/index.html Genes Required for Mitotic Spindle Assembly in S2 cells, University of California, San Francisco, USA]
 
* NHGRI Drosophila Genome Sequencing Proposals, Status of Sequencing:<br />[http://www.genome.gov/ National Human Genome Research Institute, Bethesda, MD, USA]
 
* Panther protein classification system:<br />[http://panther.appliedbiosystems.com/about.jsp Panther Protein Classification System, Applied Biosystems &amp; Celera, USA]
 
* PDB, Protein Data Bank:<br />[http://www.rcsb.org/pdb/home/home.do PDB, The Research Collaboratory for Structural Bioinformatics (RCSB) consortium]
 
* PhospoPep - phosphorylation site data from ''D. melanogaster'' cell lines:<br />[http://www.phosphopep.org/ The Aebersold group at the ETH in collaboration with the FGCZ in Switzerland, and the ISB, USA.]
 
* PubMed, Biomedical literature citations and abstracts:<br />[http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed PubMed, NCBI, Bethesda, MD USA]
 
* REDfly, Regulatory Element Database for Drosophila:<br />[http://redfly.ccr.buffalo.edu/ REDfly, University at Buffalo, New York, USA]
 
* Rfam, RNA families database of alignments and CMs:<br />[http://www.webcitation.org/getfile?fileid=db1c351a4c279e9cf9697bd2d1962097900701fb Rfam, the Sanger Institute, Cambridge, UK and Janelia Farm, Ashburn, VA, USA]
 
* TaxoDros, the database on Taxonomy of Drosophilidae:<br />[http://www.taxodros.uzh.ch/ TaxoDros, University of Zurich, Switzerland]
 
* The Drosophila Transcription Factor Database:<br />[http://www.flytf.org/ FlyTF.org, MRC Cambridge, UK]
 
* TRANSFAC, A database of transcription factors and their binding sites:<br />[http://www.gene-regulation.com/pub/databases.html#transfac TRANSFAC, Braunschweig, Germany]
 
* UniProtKB, a comprehensive catalog of information on proteins:<br />[http://www.pir.uniprot.org/ UniProtKB, The UniProt Consortium]
 
* Whole Genome Comparative Analysis of the D. melanogaster (CAF1) Genome''<nowiki>:</nowiki><br />[http://pipeline.lbl.gov/cgi-bin/gateway2?bg=droMel_caf1&selector=vistapoint Vista Tools for Comparative Genomics, LBNL, USA]
 
  
=Sequence Traces of Drosophila Genomes=
+
=Cell Lines and Cell Culture=
* ''D. ananassae'' genomic sequence trace archives:<br />[http://www.ncbi.nlm.nih.gov/Traces/trace.fcgi?cmd=retrieve&s=search&m=obtain&retrieve.x=40&retrieve.y=13&val=species_code='DROSOPHILA ANANASSAE' NCBI Trace Archives, USA]<br />[ftp://ftp.ensembl.org/pub/traces/drosophila_ananassae Ensembl FTP Trace Repository, EBI, UK]
+
* <b>Cellosaurus</b>: A thesaurus of cell lines which attempts to list all cell lines used in biomedical research.<br /> [http://web.expasy.org/cellosaurus/ Swiss Institute of Bioinformatics, Geneva, Switzerland]
* ''D. erecta'' genomic sequence trace archives:<br />[http://www.ncbi.nlm.nih.gov/Traces/trace.fcgi?cmd=retrieve&s=search&m=obtain&retrieve.x=40&retrieve.y=13&val=species_code='DROSOPHILA ERECTA' NCBI Trace Archives, USA]<br />[ftp://ftp.ensembl.org/pub/traces/drosophila_erecta Ensembl FTP Trace Repository, EBI, UK]
+
* <b>DGRC: Cell Line Catalog</b>: <br /> [https://dgrc.bio.indiana.edu/ Drosophila Genomics Resource Center, Indiana University, Bloomington, IN, USA]
* ''D. grimshawi'' genomic sequence trace archives:<br />[http://www.ncbi.nlm.nih.gov/Traces/trace.fcgi?cmd=retrieve&s=search&m=obtain&retrieve.x=40&retrieve.y=13&val=species_code='DROSOPHILA GRIMSHAWI' NCBI Trace Archives, USA]<br />[ftp://ftp.ensembl.org/pub/traces/drosophila_grimshawi Ensembl FTP Trace Repository, EBI, UK]
+
* <b>DGRC: Cell Culture Protocols</b>: <br />[https://dgrc.bio.indiana.edu/Protocols?tab=cells Drosophila Genomics Resource Center, Indiana University, Bloomington, IN, USA]
* ''D. melanogaster'' genomic sequence trace archives:<br />[http://www.ncbi.nlm.nih.gov/Traces/trace.fcgi?cmd=retrieve&s=search&m=obtain&retrieve.x=40&retrieve.y=13&val=species_code='DROSOPHILA MELANOGASTER' NCBI Trace Archives, USA]<br />[ftp://ftp.ensembl.org/pub/traces/drosophila_melanogaster Ensembl FTP Trace Repository, EBI, UK]
+
* <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]
* ''D. mojavensis'' genomic sequence trace archives:<br />[http://www.ncbi.nlm.nih.gov/Traces/trace.fcgi?cmd=retrieve&s=search&m=obtain&retrieve.x=40&retrieve.y=13&val=species_code='DROSOPHILA MOJAVENSIS' NCBI Trace Archives, USA]<br />[ftp://ftp.ensembl.org/pub/traces/drosophila_mojavensis Ensembl FTP Trace Repository, EBI, UK]
+
* <b>DGRC: Feeder Cells</b>: <br />[https://dgrc.bio.indiana.edu/cells/FeederCells Drosophila Genomics Resource Center, Indiana University, Bloomington, IN, USA]
* ''D. persimilis'' genomic sequence trace archives:<br />[http://www.ncbi.nlm.nih.gov/Traces/trace.fcgi?cmd=retrieve&s=search&m=obtain&retrieve.x=40&retrieve.y=13&val=species_code='DROSOPHILA PERSIMILIS' NCBI Trace Archives, USA]<br />[ftp://ftp.ensembl.org/pub/traces/drosophila_persimilis Ensembl FTP Trace Repository, EBI, UK]
+
* <b>DGRC: Fly Extract</b>:<br />[https://dgrc.bio.indiana.edu/cells/FlyExtract Drosophila Genomics Resource Center, Indiana University, Bloomington, IN, USA]
* ''D. pseudoobscura'' genomic sequence trace archives:<br />[http://www.ncbi.nlm.nih.gov/Traces/trace.fcgi?cmd=retrieve&s=search&m=obtain&retrieve.x=40&retrieve.y=13&val=species_code='DROSOPHILA PSEUDOOBSCURA' NCBI Trace Archives, USA]<br />[ftp://ftp.ensembl.org/pub/traces/drosophila_pseudoobscura Ensembl FTP Trace Repository, EBI, UK]
+
* <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]
* ''D. sechellia'' genomic sequence trace archives:<br />[http://www.ncbi.nlm.nih.gov/Traces/trace.fcgi?cmd=retrieve&s=search&m=obtain&retrieve.x=40&retrieve.y=13&val=species_code='DROSOPHILA SECHELLIA' NCBI Trace Archives, USA]<br />[ftp://ftp.ensembl.org/pub/traces/drosophila_sechellia Ensembl FTP Trace Repository, EBI, UK]
+
* <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]
* ''D. simulans'' genomic sequence trace archives:<br />[http://www.ncbi.nlm.nih.gov/Traces/trace.fcgi?cmd=retrieve&s=search&m=obtain&retrieve.x=40&retrieve.y=13&val=species_code='DROSOPHILA SIMULANS' NCBI Trace Archives, USA]<br />[ftp://ftp.ensembl.org/pub/traces/drosophila_simulans Ensembl FTP Trace Repository, EBI, UK]
+
* <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]
* ''D. virilis'' genomic sequence trace archives:<br />[http://www.ncbi.nlm.nih.gov/Traces/trace.fcgi?cmd=retrieve&s=search&m=obtain&retrieve.x=40&retrieve.y=13&val=species_code='DROSOPHILA VIRILIS' NCBI Trace Archives, USA]<br />[ftp://ftp.ensembl.org/pub/traces/drosophila_virilis Ensembl FTP Trace Repository, EBI, UK]
 
* ''D. willistoni'' genomic sequence trace archives:<br />[http://www.ncbi.nlm.nih.gov/Traces/trace.fcgi?cmd=retrieve&s=search&m=obtain&retrieve.x=40&retrieve.y=13&val=species_code='DROSOPHILA WILLISTONI' NCBI Trace Archives, USA]<br />[ftp://ftp.ensembl.org/pub/traces/drosophila_willistoni Ensembl FTP Trace Repository, EBI, UK]
 
* ''D. yakuba'' genomic sequence trace archives:<br />[http://www.ncbi.nlm.nih.gov/Traces/trace.fcgi?cmd=retrieve&s=search&m=obtain&retrieve.x=40&retrieve.y=13&val=species_code='DROSOPHILA YAKUBA' NCBI Trace Archives, USA]<br />[ftp://ftp.ensembl.org/pub/traces/drosophila_yakuba Ensembl FTP Trace Repository, EBI, UK]
 
  
=Genetic and Protein Interaction Databases=
+
=CRISPRs and TALENs=
* BioGRID, The General Repository for Interaction Datasets<br />[http://www.thebiogrid.org/index.php BioGRID, Mount Sinai Hospital, Toronto, Canada]
+
* <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]
* DPiM, Drosophila Protein interaction Map<br />[https://interfly.med.harvard.edu/ DPiM, Harvard University Medical School, Boston, 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]
* DroID, Drosophila Interactions Database<br />[http://www.droidb.org/ Drosophila Interaction Database, Detroit, 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]
* Drosophila PIMRider, Drosophila Protein Interaction Map<br />[https://pimr.hybrigenics.com/htmlFiles/interactionData/drosophila.html Drosophila PIMRider, Hybrigenics, Paris, France]
+
* <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]
* IM Browser, Drosophila Interactions Database<br />[http://proteome.wayne.edu/PIMdb.html IM Browser, Wayne State University, Detroit, MI, USA]
+
* <b>CRISPR fly design</b> -- reagents, protocols, and results from fly CRISPR/Cas experiments:<br />[http://www.crisprflydesign.org/ Bullolk Lab, MRC Laboratory of Molecular Biology, Cambridge, UK]
 +
* <b>CRISPR Guide Design Resources</b> CRISPR Design Tool:<br />[https://zlab.bio/guide-design-resources  Zhang Lab, MIT, Boston, MA, USA]
 +
* <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>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 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 />[http://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 />[http://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-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>, Optimal Target Finder:<br />[http://tools.flycrispr.molbio.wisc.edu/targetFinder/ 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>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 />[https://www.dpag.ox.ac.uk/research/liu-group/liu-group-news/oxfcrispr Liu lab, University of Oxford, Oxford, UK]
 +
* <b>SIFTED</b>, Specificity Inference for TAL Effector Design:<br />[https://galaxyproject.org/use/sifted/ Bulyk Lab, Harvard Medical School, 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>TRiP: Overview of sgRNA vectors</b>:<br />[https://fgr.hms.harvard.edu/sgrna-vectors TRiP, Harvard Medical School, Boston, MA, USA]
 +
 
 +
=Data Repositories=
 +
* <b>Array Express</b> - Functional Genomics Data:<br />[http://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>DDBJ</b>, the DNA Data Bank of Japan:<br />[http://www.ddbj.nig.ac.jp/ 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>ENA</b>, European Nucleotide Archive:<br />[http://www.ebi.ac.uk/embl/ 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>Ensembl Genome Browser</b>:<br />[http://useast.ensembl.org/index.html EMBL-EBI, Hinxton, UK]
 +
* <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>GenBank</b>,the NIH genetic sequence database:<br />[http://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, 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 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 />[http://www.ncbi.nlm.nih.gov/pubmed PubMed, NCBI, Bethesda, USA]
 +
* <b>PubMed Central</b>, Biomedical literature citations and abstracts:<br />[http://www.ncbi.nlm.nih.gov/pmc/ PubMed Central, NCBI, Bethesda, USA]
 +
* <b>SRA</b>, Sequence Read Archive:<br />[http://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]
 +
 
 +
=Drosophila Genomes Data and Metadata=
 +
* <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>''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. americana'' Genome</b>:<br />[https://www.ncbi.nlm.nih.gov/genome/10917 ''D. americana'' Organism Overview, NCBI, USA]<br />[http://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. 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. arizonae'' Genome</b>:<br />[http://www.ncbi.nlm.nih.gov/genome/45090/ ''D. arizonae'' Organism Overview, NCBI, USA]<br />[http://www.ncbi.nlm.nih.gov/genome/genomes/45090/ ''D. arizonae'' Genome Assembly and Annotation Report, NCBI, USA]<br />[http://www.ebi.ac.uk/ena/data/view/GCA_001654025 ''D. arizonae'' 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. 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. busckii'' Genome</b>:<br />[http://www.ncbi.nlm.nih.gov/genome/38276/ ''D. busckii'' Organism Overview, NCBI, USA]<br />[http://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. 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. 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. 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. 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. 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. 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. 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. 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. 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. navojoa'' Genome</b>:<br />[http://www.ncbi.nlm.nih.gov/genome/45091/ ''D. navojoa'' Organism Overview, NCBI, USA]<br />[http://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. 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. 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. 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. 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. 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. 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]<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 />[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. 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. 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. 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]]
 +
 
 +
=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>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>FlyAtlas2</b>, for exploring how genes are expressed in the tissues of ''D. melanogaster'':<br />[http://flyatlas.gla.ac.uk/FlyAtlas2/index.html FlyAtlas2, University of Glasgow, Glasgow, UK]
 +
* <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>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>FlyOde</b>, FLY Organ Developmental Network: <br /> [http://flyode.boun.edu.tr/index.html FlyOde, Bogazici University, Istanbul, Turkey]
 +
* <b>flytrap</b>, a database of P{GAL4} enhancer traps and their expression in brains: <br />[http://www.fly-trap.org/ flytrap, University of Edinburgh, UK]
 +
* <b>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 />[http://www.ncbi.nlm.nih.gov/geo/info/profiles.html GEO, NCBI, Bethesda, MD USA]
 +
* <b>MidExDB</b>, Drosophila CNS Midline Gene Expression Database:<br />[http://midline.bio.unc.edu/MDB_Home.aspx Crews laboratory, University of North Carolina, Chapel Hill, 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>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=
 +
* <b>FlyBase Gene Groups</b>, Manually curated reports on functionally related genes, based on the literature:<br /> [http://flybase.org/lists/FBgg/ Gene group list, FlyBase]
 +
* <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>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>Interactive fly</b>, Drosophila genes listed by biochemical function:<br /> [http://www.sdbonline.org/sites/fly/aimain/6biochem.htm Interactive Fly, Thomas Brody and Society for Developmental Biology, MD, USA]
 +
* <b>Interactive fly</b>, Maternally transcribed genes:<br /> [http://www.sdbonline.org/sites/fly/aimain/4matrnl.htm Interactive Fly, Thomas Brody and Society for Developmental Biology, MD, USA]
 +
* <b>Interactive fly</b>, Zygotically transcribed genes:<br /> [http://www.sdbonline.org/sites/fly/aimain/5zygotic.htm Interactive Fly, Thomas Brody and Society for Developmental Biology, MD, USA]
 +
* <b>KEGG BRITE</b>, Functional hierarchies and binary relationships of biological entities:<br /> [http://www.genome.jp/kegg/brite.html KEGG, Kyoto University, Kyoto, Japan and University of Tokyo, Tokyo, Japan]
 +
* <b>UCSC D. melanogaster Gene Sorter</b>, displays tables of genes related by a variety of characteristics including protein-level homology, similarity of gene expression profiles, and genomic proximity.:<br /> [https://genome.ucsc.edu/cgi-bin/hgNear?org=D.+melanogaster UCSC Genome Informatics Group, University of California, Santa Cruz, Santa Cruz, CA, USA]
 +
 
 +
=General Bioinformatics Tools=
 +
* <b>Bioconductor</b>, Open Source Software for Bioinformatics:<br />[http://www.bioconductor.org/ Fred Hutchinson Cancer Research Center, Seattle, USA]
 +
* <b>BioMart</b>, Data Warehouse:<br />[http://www.biomart.org/ 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>Cytoscape</b> -- Network Data Integration, Analysis, and Visualization in a Box:<br />[http://www.cytoscape.org/ Cytoscape, Cytoscape Consortium, Canada, France, and USA]
 +
* <b>FlyMine</b>, an Integrated Database for Drosophila and Anopheles Genomics:<br />[http://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>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]
 +
 
 +
=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]
 +
 
 +
=Human Disease: Drosophila Models and Orthologous Genes=
 +
* <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>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 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>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>ModelMatcher</b>, Connecting clinicians and scientists to study rare and undiagnosed diseases:<br />[https://www.modelmatcher.net/ 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.]
 +
 
 +
=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>COMPLEAT</b>, protein COMPLex Enrichment Analysis Tool:<br />[http://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>DroID</b>, Drosophila Interactions Database:<br />[http://www.droidb.org/ Drosophila Interaction Database, Detroit, USA]
 +
* <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>FlyOde</b>, FLY Organ Developmental Network: <br /> [http://flyode.boun.edu.tr/index.html FlyOde, Bogazici University, Istanbul, Turkey]
 +
* <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>IntAct</b>, Molecular Interaction Database:<br />[http://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>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 />[http://www.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>STRING</b>, Known and Predicted Protein-Protein Interactions<br />[http://string-db.org/ STRING, SIB, Switzerland CPR, Denmark, and EMBL, Heidelberg, Germany]
 +
* <b>WikiPathways</b>, an open, public platform dedicated to the curation of biological pathways by and for the scientific community:<br />[http://www.wikipathways.org/index.php/WikiPathways WikiPathways, Gladstone Institute, San Francisco, CA, USA and Maastricht University, The Netherlands]
 +
 
 +
=Laboratory Resources=
 +
* <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]
 +
 
 +
=Metabolomics=
 +
* <b>FlyMet</b>, A Tissue- and Sex-Specific Metabolomic Atlas and Database :<br />[http://www.flymet.org/ FlyMet, University of Glasgow, Glasgow, Scotland]
 +
 
 +
=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>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://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 />[http://www.ou.edu/journals/dis/ DIS, Norman, Oklahoma, USA]
 +
* <b>Drosophilids of the Midwest and Northeast</b>:<br />[https://digitalcommons.mtu.edu/oabooks/1/ by T. Werner, 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 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>FlyTree</b>, the Drosophila Researcher Genealogy has been incorporated into the Academic Tree Project: <br />[http://www.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>Gene Lookup</b>, Gene and Reagent Lookup:<br />[http://www.flyrnai.org/cgi-bin/DRSC_gene_lookup.pl Gene Lookup, DRSC, Harvard Medical School, Boston, MA, USA]
 +
* <b>IGTRCN</b>, Insect Genetic Technologies Research Coordination Network:<br />[http://igtrcn.org// IGTRCN, University of Maryland, Rockville, MD, USA]
 +
* <b>Interactive Fly</b>, A cyberspace guide to Drosophila development and metazoan evolution<br />[http://www.sdbonline.org/fly/aimain/1aahome.htm Interactive Fly, Bethesda, MD, USA]
 +
* <b>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>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>MitoDrome</b>, ''Drosophila melanogaster'' nuclear genes encoding for mitochondrial proteins:<br />[http://mitodrome.ba.itb.cnr.it/ MitoDrome, Bari, Italy]
 +
* <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>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=
 +
 
 +
==General==
 +
* <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 />[http://rfam.xfam.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]
 +
 
 +
==lncRNA==
 +
* <b>LNCediting</b>, Function of RNA editing in lncRNAs :<br />[http://bioinfo.life.hust.edu.cn/LNCediting/ LNCediting, Huazhong University of Science and Technology, Wuhan, China and University of Texas, Houston, Texas, USA]
 +
 
 +
==miRNA==
 +
===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 />
 +
::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>Tools4miRs</b>, Manually curated platform gathering methods for the broadly-defined miRNA analysis (last updated 2019):<br />[https://tools4mirs.org/ Tools4miRs, Polish Academy of Sciences and University of Warsaw, Warsaw, Poland]
 +
* <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
 +
 
 +
===miRNA Target Prediction===
 +
* <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>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>miRWalk - The Database on Predicted and Validated microRNA Targets</b> :<br />[http://zmf.umm.uni-heidelberg.de/apps/zmf/mirwalk/micrornapredictedtarget.html miRNA - Target Prediction, Ruprecht-Karls-Universität Heidelberg, Medizinische Fakultät Mannheim, Germany]
 +
* <b>TargetScanFly</b>, Prediction of microRNA targets based on miRNA seed region and target conservation (last updated 2012):<br />[http://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 />[http://carolina.imis.athena-innovation.gr/diana_tools/web/index.php?r=tarbasev8%2Findex DIANA TarBase, DIANA LAB, Athens, Greece]
 +
* <b>miRecords</b>, A database of experimentally validated miRNA targets curated from literature (last updated 2009):<br />[http://c1.accurascience.com/miRecords/ miRecords, University of Minnesota, Minneapolis, MN, USA]
 +
* <b>miRTex</b>, A text-mining system that extracts miRNA-gene regulation relations and miRNA-target relations from literature (last updated 2017):<br />[http://research.bioinformatics.udel.edu/miRTex/ miRTex, University of Delaware, Newark, DE, USA]
 +
 
 +
===Comparative miRNA Analysis===
 +
* <b>CoGemiR</b>, Comparative Genomics Analysis of MicroRNA (last updated 2008):<br />[http://cogemir.tigem.it/htdocs/index.html CoGemiR, Telethon Institute of Genetics and Medicine, Naples, Italy]
 +
* <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]
 +
* <b>miROrtho</b>, Predictions of precursor miRNA genes covering several animal genomes combining orthology and a Support Vector Machine (last updated 2009):<br />[http://cegg.unige.ch/mirortho miROrtho, University of Geneva, Geneva, Switzerland]
 +
 
 +
==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>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>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 ]
 +
==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=
 +
* <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 (DO)</b>, ontology of disease terms:<br />[http://disease-ontology.org/ Disease Ontology]
 +
* <b>Gene Ontology Consortium (GO)</b><br />[http://geneontology.org/ Gene Ontology Consortium]
 +
* <b>GOrilla</b> -- Gene Ontology enRIchment and anaLysis and viuaLizAtion tool:<br />[http://cbl-gorilla.cs.technion.ac.il/ GOrilla, Israel]
 +
* <b>OboEdit</b>, browser for OBO ontologies:<br />[http://oboedit.org/ OboEdit]
 +
* <b>The OBO Foundry</b>, an ontology registry:<br />[http://obofoundry.github.io/ OboFoundry]
 +
* <b>Ontobee</b>, an ontologies browser:<br />[http://www.ontobee.org/ Ontobee, He Group, University of Michigan Medical School, Ann Arbor, Michigan, USA]
 +
* <b>Ontology Lookup Service</b>, an ontologies browser:<br />[http://www.ebi.ac.uk/ontology-lookup/ Ontology Lookup Service, EMBL-EBI, Hinxton, UK]
 +
* <b>Protege</b>, browser for OWL ontologies:<br />[http://protege.stanford.edu/products.php Protege, Stanford Center for Biomedical Informatics Research, Stanford University School of Medicine, USA]
 +
* <b>QuickGO</b>, a browser for Gene Ontology terms and annotations:<br />[http://www.ebi.ac.uk/QuickGO/ QuickGO, EMBL-EBI, Hinxton, UK]
 +
 
 +
=Orthology Predictions=
 +
* <b>Compara</b>, Ensembl Compara provides cross-species resources and analyses, at both the sequence level and the gene level.<br />[http://useast.ensembl.org/info/genome/compara/index.html?redirect=no Ensembl, Hinxton, UK]
 +
* <b>DIOPT</b>, DRSC Integrative Ortholog Prediction Tool<br />[http://www.flyrnai.org/cgi-bin/DRSC_orthologs.pl DRSC/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>EggNOG</b>, A database of orthologous groups and functional annotation:<br />[http://eggnogdb.embl.de/#/app/home Computational Biology Group, EMBL, Heidelberg, Germany]
 +
* <b>Gene2Function</b>:<br /> [http://www.gene2function.org/search/ Gene2Function, Harvard Medical School, Boston, MA, 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 />[http://www.ncbi.nlm.nih.gov/homologene NCBI, Bethesda, MD, USA]
 +
* <b>Inparanoid</b>, InParanoid: ortholog groups with inparalogs<br />[http://inparanoid.sbc.su.se/cgi-bin/index.cgi Stockholm Bioinformatics Centre, Stockholm, Sweden]
 +
* <b>Isobase</b>, A Database of Functionally Related Orthologs, which incorporates PPI network data in addition to sequence similarity.<br />[http://groups.csail.mit.edu/cb/mna/isobase/ MIT, Cambridge, MA, USA]
 +
* <b>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>OrthoDB</b>, The Hierarchical Catalog of Orthologs<br />[https://www.orthodb.org/ Zdobnov Computational Evolutionary Genomics group, University of Geneva, Geneva, Switzerland]
 +
* <b>OrthoMCL</b>, Ortholog Groups of Protein Sequences<br />[http://www.orthomcl.org/orthomcl/ EuPathDB]
 +
* <b>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>Roundup</b>, A large-scale orthology database using the Reciprocal Smallest Distance (RSD) algorithm.<br />[http://wall-lab.stanford.edu/projects/roundup/ Wall lab, Stanford University, Palo Alto, CA, USA]
 +
* <b>TreeFam</b>, A database composed of phylogenetic trees inferred from animal genomes. It provides orthology/parology predictions as well the evolutionary history of genes.<br />[http://www.treefam.org/ EMBL-EBI, Hinxton, UK]
 +
 
 +
=Phylogenetic Comparison Tools=
 +
* <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>EvoPrinter</b>, Identification of Evolutionarily Resilient DNA Sequences<br />[http://evoprinter.ninds.nih.gov/ NINDS, NIH, Bethesda MD, USA]
 +
* <b>HomoloGene</b> -- automated system fo constructing putative homology groups:<br />[http://www.ncbi.nlm.nih.gov/homologene NCBI, Bethesda, MA, USA]
 +
* <b>InParanoid</b>, Eukaryotic Ortholog Groups:<br />[http://inparanoid.sbc.su.se/cgi-bin/index.cgi InParanoid, Karolinska Institute, Sweden]
 +
* <b>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>OrthoDB</b>, the Hierarchical Catalog of Orthologs:<br />[http://www.orthodb.org/ OrthoDB, University of Geneva, Switzerland]
 +
* <b>flyDIVaS</b>, a comparative genomics database resource of ''Drosophila'' divergence and selection: <br />[http://129.32.209.132/index.html 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=
 +
* <b>BDGP Single Nucleotide Polymorphism (SNP) Project</b>:<br />[http://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 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 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 />[http://wfitch.bio.uci.edu/~dspr/index.html DSPR, University of Kansas and UC Irvine, USA]
 +
* <b>FlyVar Project</b>: A Database of Drosophila Genetics Variations <br />[http://www.iipl.fudan.edu.cn/FlyVar/ FlyVar, Fudan University, Shanghai, China and Baylor College of Medicine, Houston, TX, USA]
 +
* <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 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>GPCRDB</b>, information system for G protein-coupled receptors (GPCRs):<br />[http://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>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 />[http://merops.sanger.ac.uk/ MEROPS, Wellcome Trust Sanger Institute, Hinxton, UK]
 +
* <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>Panther (Protein Analysis THrough Evolutionary Relationships)</b> protein classification system:<br />[http://panther.appliedbiosystems.com/about.jsp Panther Protein Classification System, Applied Biosystems &amp; Celera, USA]
 +
* <b>PDB</b>, Protein Data Bank:<br />[http://www.rcsb.org/pdb/home/home.do PDB, The Research Collaboratory for Structural Bioinformatics (RCSB) consortium]
 +
* <b>PhospoPep</b>, Protein Phosphorylation Database: <br />[http://www.phosphopep.org/index.php 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>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>UniProtKB</b>, a comprehensive catalog of information on proteins:<br />[https://www.uniprot.org/uniprot/ UniProtKB, The UniProt Consortium]
 +
 
 +
=Public Education=
 +
* <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>''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>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>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=
 +
* <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>Search by gene(s) to find hit information for genes and DRSC amplicons in DRSC screens</b>:<br /> [http://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>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>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>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>RNAiCut</b>, Automated Detection of Significant Genes from Functional Genomic Screens:<br /> [http://rnaicut.csail.mit.edu/ 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>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>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>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>VDRC</b>, Vienna Drosophila Resource Center: <br />[http://stockcenter.vdrc.at/control/main Genome-wide transgenic Drosophila RNAi libraries, VDRC, Vienna, Austria]
  
 
=Sequence Analysis=
 
=Sequence Analysis=
* cis-analyst, to search the Drosophila genome for clusters of binding sites: <br />[http://rana.lbl.gov/cis-analyst/ cis-analyst, 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]
* FlyPrimerBank, a comprehensive qPCR primer database for Drosophila: <br />[http://www.flyrnai.org/FlyPrimerBank FlyPrimerBank, DRSC, Harvard Medical School, Boston, MA, 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]
* FGENESH, Annotation of animal genomes-genes, promoters, functional motifs, protein sub-cellular localization.:<br />[http://www.softberry.com/berry.phtml?topic=case_study_animal&no_menu=on Annotation of genomes, Softberry, USA]
+
* <b>FlyPrimerBank</b>, a comprehensive qPCR primer database for Drosophila: <br />[http://www.flyrnai.org/FlyPrimerBank FlyPrimerBank, DRSC, Harvard Medical School, Boston, MA, USA]
* GenePalette, a tool for genome sequence visualization and navigation: <br />[http://www.genepalette.org/ GenePalette, University of California, San Diego, 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]
* Genie Gene finder for Drosophila:<br />[http://www.fruitfly.org/seq_tools/genie.html Genie, Berkeley Drosophila Genome Project, University of California, Berkeley, USA]
+
* <b>GenePalette</b>, a tool for genome sequence visualization and navigation: <br />[http://www.genepalette.org/ GenePalette, University of California, San Diego, USA]
* miRNA, Target Gene Prediction:<br />[http://www.mirna.embl.de/ miRNA - Target Prediction, EMBL, Heidelberg, Germany]
+
* <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]
* miRNA_Targets:<br />[http://mamsap.it.deakin.edu.au/~amitkuma/mirna_targetsnew/index.html miRNA targets on full length mRNAs, Deakin University, Victoria, Australia]
+
* <b>HRMA</b> -- High Resolution Melt Analysis: <br /> [http://www.flyrnai.org/hrma HRMA, DRSC, Harvard Medical School, Boston, MA, USA]
* Neural Network Promoter Prediction for Drosophila:<br />[http://www.fruitfly.org/seq_tools/promoter.html Neural Network Promoter Prediction, Berkeley Drosophila Genome Project, University of California, Berkeley, USA]
+
* <b>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]
* PREdictor, to identify Polycomb/Trithorax response elements: <br />[http://bibiserv.techfak.uni-bielefeld.de/predictor/ PREdictor, Bielefeld University, Germany]
+
* <b>RepeatMasker</b>: <br />[http://www.repeatmasker.org/ RepeatMasker Institute for Systems Biology, Seattle, WA, USA]
* Splice Site Prediction for Drosophila:<br />[http://www.fruitfly.org/seq_tools/splice.html Splice Site Prediction, Berkeley Drosophila Genome Project, University of California, Berkeley, USA]
+
* <b>Splice Site Prediction for Drosophila</b>:<br />[http://www.fruitfly.org/seq_tools/splice.html Splice Site Prediction, Berkeley Drosophila Genome Project, University of California, Berkeley, USA]
* UP-TORR Fly, a tool for identifying updated targets of RNAi reagents: <br />[http://www.flyrnai.org/up-torr/ Updated Targets of RNAi Reagents, DRSC, Harvard Medical School, Boston, MA,USA]
+
* <b>Web Apollo</b>, a collaborative genomic annotation editor: <br />[http://apollo.berkeleybop.org/ Web Apollo, LBL, Berkeley, USA]
* Web Apollo, a collaborative genomic annotation editor: <br />[http://apollo.berkeleybop.org/ Web Apollo]
+
 
 +
=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://asap.epfl.ch/ 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]
  
=Atlases, Images, and Videos=
+
* <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]
* BDTNP, A cellular resolution 3D gene expression and morphology Atlas of the blastoderm.<br />[http://bdtnp.lbl.gov/Fly-Net/bioimaging.jsp?w=summary Berkeley Drosophila Transcription Network Project, University of California, Berkeley, USA]
 
* CSIRO Entomology Anatomical Atlas of Flies:<br />[http://www.ento.csiro.au/biology/fly/fly.html# CSIRO Entomology, Australia]
 
* Electron micrograph maps of ''Drosophila melanogaster'' polytene chromosomes:<br />[http://www.helsinki.fi/~saura/EM/index.html Sorsa Maps, Helsinki, Finland]
 
* Fly Motor Axon Page:<br />[http://www.its.caltech.edu/~zinnlab/motoraxons/fma home page.html Motor Axon, California Institute of Technology, USA]
 
* FlyBrain, an Online Atlas and Database of the Drosophila Nervous System:<br />[http://flybrain.neurobio.arizona.edu/ FlyBrain, University of Arizona, Tucson, USA]
 
* FlyCircuit, a Database of Drosophila Brain Neurons:<br />[http://www.flycircuit.tw/ FlyCircuit, National Tsing Hua University, Taiwan]
 
* FlyEx, a Database of Segmentation Gene Expression in Drosophila:<br />[http://urchin.spbcas.ru/flyex/ FlyEx, St. Petersburg State Polytechnical University, Russia]<br />[http://flyex.ams.sunysb.edu/FlyEx/ FlyEx, Stony Brook University, USA]
 
* FlyExpress, an Expression Pattern Search Engine:<br />[http://www.flyexpress.net/ FlyExpress, Arizona State University, USA]
 
* FlyLight, Expression Patterns of GAL4 Driver Lines:<br />[http://flweb.janelia.org/cgi-bin/flew.cgi HHMI, Janelia Farms Research Campus]
 
* FlyMove, an Image, Movie and Interactive Shockwave Resource:<br />[http://flymove.uni-muenster.de/ FlyMove, Muenster, Germany]
 
* FlyTrap, a GFP Protein Trap Database:<br />[http://flytrap.med.yale.edu/ FlyTrap, Yale University, USA]
 
* flytrap, a database of P{GAL4} enhancer traps and their expression in brains: <br />[http://www.fly-trap.org/ flytrap, University of Edinburgh, UK]
 
* FlyView, a Drosophila Image Database:<br />[http://flyview.uni-muenster.de/ FlyView, Muenster, Germany]
 
* GETDB, a Gal4 enhancer trap database:<br />[http://flymap.lab.nig.ac.jp/~dclust/getdb.html GETDB, National Institute of Basic Biology, Okazaki, Japan]
 
* Jove, videos of experimental techniques:<br />[http://www.jove.com/index/browse.stp?Search=Drosophila Jove, Journal of Visualized Experiments, USA]
 
* Patterns of gene expression in Drosophila embryogenesis:<br />[http://www.fruitfly.org/cgi-bin/ex/insitu.pl Gene expression database, BDGP, USA]
 
* Scans of Bridges' original 1935 polytene drawings for ''D. melanogaster''<nowiki>:</nowiki><br />[http://www.hawaii.edu/bio/Chromosomes/poly/poly.html GEM Website, University of Hawaii, USA]
 
* Virtual Fly Brain - A 3D brain browser with point and click searches for neurons, transgenes and phenotypes:<br />[http://www.virtualflybrain.org Edinburgh &amp; Cambridge, UK]
 
  
=Other=
+
=Taxonomy=
* Drosophila Information Service:<br />[http://www.ou.edu/journals/dis/ DIS, Norman, Oklahoma, USA]
+
* <b>Taxonomy of Drosophilidae</b> -- Collection of Papers:<br />[http://www.drosophila.jp/jdd/index_en.html Japan Drosophila Database (JDD) on Taxonomy, Japan]
* FlyNome, a database of Drosophila nomenclature: <br />[http://www.flynome.com/index.html FlyNome, USA]
+
* <b>FlyPhenomics</b>, phenotypic differences between species of the ''D. melanogaster'' subgroup:<br />[http://www.normalesup.org/~vorgogoz/FlyPhenomics/ FlyPhenomics, Paris, France]
* FlyPNS, embryonic and larval peripheral nervous system: <br />[http://www.normalesup.org/~vorgogoz/FlyPNS/page1.html FlyPNS, USA]
+
* <b>TaxoDros</b> Drosophilidae Taxonomic Database:<br />[https://bioinfo.museum.hokudai.ac.jp/ Drosophilidae Taxonomic Database, Japan]
* FlyTree, the Drosophila Researcher Genealogy has been incorporated into the Academic Tree Project: <br />[http://www.academictree.org/flytree/ FlyTree, USA]
+
* <b>TaxoDros</b>, the database on Taxonomy of Drosophilidae:<br />[http://www.taxodros.uzh.ch/ TaxoDros, University of Zurich, Switzerland]
* Interactive Fly, A cyberspace guide to Drosophila development and metazoan evolution<br />[http://www.sdbonline.org/fly/aimain/1aahome.htm Interactive Fly, Bethesda, MD, USA]
+
* <b>Taxonomy</b>, NCBI Taxonomy Database:<br />[http://www.ncbi.nlm.nih.gov/taxonomy NCBI, Bethesda, MD USA]
* Jfly , a data depository for the fly and other insects, with an emphasis for the Japanese-speaking fly community:<br />[http://jfly.iam.u-tokyo.ac.jp/ Jfly, University of Tokyo, Japan]
 
* The WWW Virtual Library--Drosophila:<br />[http://www.ceolas.org/fly/ Drosophila Virtual Library]
 
* Tracheal Database, information on tracheal development in Drosophila: <br />[http://www.biozentrum.unibas.ch/affolter/trachea/ Tracheal Database, Switzerland]
 
  
 +
=Transcription Regulation Databases and Tools=
 +
* <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>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>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>EPD</b>, the Eukaryotic Promoter Database:<br />[http://epd.vital-it.ch/drosophila/drosophila_database.php/ EPD, Epalinges s/Lausanne, Switzerland]
 +
* <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>FlyReg</b>, DNase I Footprint Database:<br />[http://www.flyreg.org/ University of Manchester Bioinformatics Resources, University of Manchester, UK]
 +
* <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 />[http://jaspar.genereg.net/ JASPAR]
 +
* <b>FlyReg</b>, DNase I Footprint Database:<br />[http://www.flyreg.org/ University of Manchester Bioinformatics Resources, University of Manchester, 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, CA, 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, NY, 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>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>TRANSFAC</b>, A database of transcription factors and their binding sites:<br />[http://www.gene-regulation.com/pub/databases.html#transfac TRANSFAC, Braunschweig, 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]
  
 +
=Suggest a tool or resource=
 +
*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 19:40, 10 June 2021

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

Genome Sequencing Projects

Human Disease: Drosophila Models and Orthologous Genes

Interaction and Pathway Databases

Laboratory Resources

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.

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