Difference between revisions of "FlyBase:Drosophila Network Resources"

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=Related Projects=
+
=Atlases, Images and Videos=
:[http://www.gmod.org/ GMOD]
+
* <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]
:[http://www.geneontology.org/ Gene Ontology (GO)]
+
* <b>BDTNP</b>, A cellular resolution 3D gene expression and morphology Atlas of the blastoderm:<br />[http://bdtnp.lbl.gov/Fly-Net/bioimaging.jsp?w=summary Berkeley Drosophila Transcription Network Project, University of California, Berkeley, USA]
:[http://www.genomeknowledge.org/ Reactome]
+
* <b>BrainTrap</b>, A collection of 3D confocal datasets taken from EYFP expressing protein trap Drosophila lines from the Cambridge Protein Trap project: <br />[http://fruitfly.inf.ed.ac.uk/braintrap/ Armstrong Lab, University of Edinburgh, Edinburgh, UK]
:[http://www.fruitfly.org/ BDGP (Berkeley Drosophila Genome Project)]
+
* <b>CSIRO</b> Anatomical Atlas of Flies:<br />[http://www.ento.csiro.au/biology/fly/fly.html# CSIRO Entomology, Australia]
:[http://dgrc.cgb.indiana.edu/ DGRC (Drosophila Genomics Resource Center)]
+
* <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]
:[http://www.ou.edu/journals/dis/byissue.html DIS by issue]
+
* <b>FlyCircuit</b>, a Database of Drosophila Brain Neurons:<br />[http://www.flycircuit.tw/ FlyCircuit, National Tsing Hua University, Taiwan]
:[http://www.flyexpress.net/ FlyExpress]
+
* <b>FlyMove</b>, an Image, Movie and Interactive Shockwave Resource:<br />[http://flymove.uni-muenster.de/ FlyMove, Muenster, Germany]
:[http://www.sdbonline.org/fly/aimain/1aahome.htm Interactive Fly]
+
* <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]
:[http://www.modencode.org/ modENCODE]
+
* <b>FlyView</b>, a Drosophila Image Database:<br />[http://flyview.uni-muenster.de/ FlyView, Muenster, Germany]
:[http://www.textpresso.org/fly/ Textpresso for Fly]
+
* <b>GETDB</b>, a Gal4 enhancer trap database:<br />[https://kyotofly.kit.jp/stocks/GETDB/getdb.html GETDB, Kyoto Institute of Technology, Kyoto, Japan]
 +
* <b>Interactive Maps</b>: four maps displaying markers and lineages of ''D. melanogaster'' neuroblasts, glial cells, and interneurons:<br />[http://www.genetik.biologie.uni-mainz.de/106.php Interactive Maps, Institut fur Genetik, Johannes Gutenberg University, Mainz, Germany]
 +
* <b>Jove</b>, videos of experimental techniques:<br />[http://www.jove.com/index/browse.stp?Search=Drosophila Jove, Journal of Visualized Experiments, USA]
 +
* <b>Learning to Fly</b>, a poster showing photographs of commonly used marker phenotypes in D. melanogaster:<br />[http://onlinelibrary.wiley.com/journal/10.1002/%28ISSN%291526-968X/homepage/free_posters.htm Genesis (Journal), Wiley Online Library]
 +
* <b>PeptideAtlas</b>, a multi-organism, publicly accessible compendium of peptides identified in a large set of tandem mass spectrometry proteomics experiments: <br />[http://www.peptideatlas.org/ Seattle Proteome Center, Seattle, Washington, USA]
 +
* <b>Virtual Fly Brain</b> - A 3D brain browser with point and click searches for neurons, transgenes and phenotypes:<br />[http://www.virtualflybrain.org Virtual Fly Brain, Edinburgh and Cambridge, UK]
  
=Stock Collections=
+
=CRISPRs and TALENs=
===''D. melanogaster'' Collections===
+
* <b>CCTop</b> CRISPR/Cas9 optimum target finder:<br />[http://crispr.cos.uni-heidelberg.de/ Center for Organismal Studies, Heidelberg University, Heidelberg, DE]
:[http://flystocks.bio.indiana.edu/ Bloomington]
+
* <b>CHOPCHOP</b> CRISPR/Cas9 target online predictor, mammalian and other major model organisms including fly:<br />[http://chopchop.cbu.uib.no// Schier Lab, Harvard University, Cambridge, MA, Church Lab, Harvard Medical School, Boston, MA, USA]
:[http://www.drosdel.org.uk/ DrosDel]
+
* <b>CRISPR/Cas Web Resources</b> Web Resources for design and planning of CRISPR/Cas9 studies:<br />[http://igtrcn.org/knowledgebase/crisprcas-web-resources// IGTRCN, Insect Genetic Technologies Research Coordination Network, University of Maryland, Rockville, MD, USA]
:[http://drosophila.med.harvard.edu/ Exelixis (Harvard)]
+
* <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]
:[http://flypush.imgen.bcm.tmc.edu/pscreen/ GDP (Baylor)]
+
* <b>CRISPR Genome Engineering Resources</b> CRISPR Design Tool:<br />[http://www.genome-engineering.org/crispr/?page_id=41/  Zhang Lab, MIT, Boston, MA, USA]
:[http://www.dgrc.kit.ac.jp/ Kyoto]
+
* <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]
:[http://www.shigen.nig.ac.jp/fly/nigfly/ NIG-Fly]
+
* <b>CRISPRscan</b> Novel scoring algorithm for selecting sgRNAs<br />[http://www.crisprscan.org// Giraldez Lab, Yale University, New Haven, CT, USA]
:[http://stockcenter.vdrc.at/control/main VDRC]
+
* <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 Finding CRISPRs</b>, Drosophila CRISPR gRNA design search tool:<br />[http://www.flyrnai.org/crispr2/ DRSC/TRiP-FGR, Harvard Medical School, Boston, MA, USA]
 +
* <b>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>ZiFiT Targeter</b>, Tool for Identifying Zinc Finger Nuclease Sites in Specific Target Sequences:<br />[http://zifit.partners.org/ZiFiT/ MGH and Harvard Medical School, Boston, MA]
  
===Species Collections===
+
=Data Repositories=
:[http://kyotofly.kit.jp/cgi-bin/ehime/index.cgi Ehime]
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* <b>Array Express</b> - Functional Genomics Data:<br />[http://www.ebi.ac.uk/arrayexpress/ Array Express, EMBL-EBI, Hinxton, UK]
:[https://stockcenter.ucsd.edu/info/welcome.php UC San Diego]
+
* <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]
  
===Other public collections===
+
=Drosophila Genomes Data and Metadata=
:'''Drosophila Gene Search Project'''
+
* <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]
:Information about ordering P{GS} lines can be found at http://gsdb.biol.metro-u.ac.jp/~dclust/index.html
+
* <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]]
  
:'''Ehime Drosophila Species Stock Center of Japan'''
+
=Gene Expression Databases and Tools=
:A collection of wild-type strains of D. melanogaster and strains of some 30 species can be found at http://kyotofly.kit.ac.jp/ehime/
+
* <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>BDTNP</b>, A cellular resolution 3D gene expression and morphology Atlas of the blastoderm.<br />[http://bdtnp.lbl.gov/Fly-Net/bioimaging.jsp?w=summary Berkeley Drosophila Transcription Network Project, University of California, Berkeley, USA]
 +
* <b>BGee</b> Normal Gene Expression Data in Animals (based on RNA-Seq, Affymetrix, in situ hybridization, and EST data).<br />[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/flyatlas/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]
  
:'''FlyTrap Stock Collection'''
+
=Gene Groups=
:GFP protein trap lines from the FlyTrap project can be obtained at Yale University, USA at http://flytrap.med.yale.edu/
+
* <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]
  
:'''FlyView Stock Collection'''
+
=General Bioinformatics Tools=
:Enhancer trap lines from the FlyView project can be obtained at University of Muenster, Germany at http://flyview.uni-muenster.de/
+
* <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>DNA & Protein Work List</b>, A list of tools aggregated by the Prokop Lab:<br />[http://www.prokop.co.uk/Links/tools.html http://www.prokop.co.uk/Links/tools.html]
 +
* <b>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]
  
:'''Kyorin-Fly'''
+
=Genome Sequencing Projects=
:A collection of mutant and wildtype stocks of Drosophila species, especially the Drosophila ananassae species subgroup, D. auraria complex, and D. hydei. http://kyotofly.kit.jp/cgi-bin/kyorin/index.cgi
+
* <b>''D. pseudoobscura'' genome project</b>:<br />[https://www.hgsc.bcm.edu/arthropods/drosophila-pseudoobscura-genome-project D. pseudoobscura Human Genome Sequencing Center, Baylor College of Medicine, USA]
 +
* <b>D. simulans and yakuba sequencing projects</b>:<br />[http://www.dpgp.org/sim_yak/index.html DPGP, University of California, Davis, USA]
  
:'''Tübingen Drosophila Stock Collection'''
+
=Human Disease: Drosophila Models and Orthologous Genes=
:A list of approximately 2,000 Drosophila stocks at the Max-Planck-Institute for Developmental Biology.
+
* <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>HuDis</b>, high confidence human disease gene - fly gene ortholog pairs:<br />[http://www.flyrnai.org/HuDis DRSC/TRiP-FGR, Harvard Medical School, Boston, MA, USA]
 +
* <b>MORPHIN</b>, Model ORganism Projected on a Human Integrated gene Network:<br />[http://www.inetbio.org/morphin/index.php MORPHIN, Lee Lab, Yonsei University, Korea and Marcotte Lab, University of Texas at Austin, USA.]
 +
* <b>NeuroGeM</b>, A knowledgebase of genetic modifiers in neurodegenerative diseases:<br />[http://chibi.ubc.ca/neurogem/ CHiBi, The University of British Columbia, Vancouver, BC, Canada]
  
:'''UC San Diego Drosophila Stock Center'''
+
=Interaction and Pathway Databases=
:Approximately 270 different Drosophila species at University of San Diego, USA can be obtained at https://stockcenter.ucsd.edu/info/welcome.php
+
* <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>DAPPER</b>, database for protein-protein interactions:<br/>[http://dapper.gen.cam.ac.uk/ DAPPER, University of Cambridge, Cambridge, UK]
 +
* <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>Drosophila PIMRider</b>, Drosophila Protein Interaction Map:<br />[https://pimr.hybrigenics.com/htmlFiles/interactionData/drosophila.html Drosophila PIMRider, Hybrigenics, Paris, France]
 +
* <b>FlyBase Signaling Pathways</b>, Manually curated reports on Signaling Pathways, based on the literature:<br /> [http://flybase.org/lists/FBgg/pathways Pathways list, FlyBase]
 +
* <b>FlyCyc</b> -- Curated Drosophila melanogaster Pathways:<br />[http://biocyc.org/FLY/organism-summary?object=FLY FlyCyc, Harvard University, Cambridge, USA]
 +
* <b>FlyNet Gene Prioritization</b>: <br /> [http://www.inetbio.org/flynet/Network_gene_prioritization.php NetBioLab, Yonsei University, Seoul, Korea]
 +
* <b>FlyOde</b>, FLY Organ Developmental Network: <br /> [http://flyode.boun.edu.tr/index.html FlyOde, Bogazici University, Istanbul, Turkey]
 +
* <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>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]
  
:'''University of Cambridge FlyProt project'''
+
=Laboratory Resources=
:Annotations, expression patterns and sequence data for the YFP protein trap lines from the FlyProt project can be viewed on the Flannotator at http://www.flyprot.org. Stocks are available from the Kyoto Stock Center.
+
* <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]
  
=Vectors and Constructs=
+
=Miscellaneous=
http://flybase.org/static_pages/lists/vectors.html
+
* <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 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, Outreach resources</b> - A compendium of information on ''Drosophila melanogaster'' as a model organism:<br />[http://www.flyfacility.ls.manchester.ac.uk/forthepublic/outreachresources/ University of Manchester, Manchester, UK]
 +
* <b>MitoDrome</b>, ''Drosophila melanogaster'' nuclear genes encoding for mitochondrial proteins:<br />[http://mitodrome.ba.itb.cnr.it/ MitoDrome, Bari, Italy]
 +
* <b>Mitotic Spindle Assembly Database</b>:<br />[http://rnai.ucsf.edu/mitospindlescreen/index.html Genes Required for Mitotic Spindle Assembly in S2 cells, University of California, San Francisco, USA]
 +
* <b>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>PhospoPep</b> -- phosphorylation site data from ''D. melanogaster'' cell lines:<br />[http://www.phosphopep.org/ The Aebersold group at the ETH in collaboration with the FGCZ in Switzerland, and the ISB, USA.]
 +
* <b>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]
  
=Listing of all resources=
+
=Non-coding (ncRNA) Databases and Tools=
==Drosophila Network Resources==
 
===Comparative Analyses and Genome Databases===
 
  
    Assembly/Alignment/Annotation of 12 related Drosophila species:
+
==General==
    »Assembly/Alignment/Annotation, LBNL, USA
+
* <b>NONCODE</b>, An integrated knowledge database dedicated to ncRNAs, especially lncRNAs (last updated 2017):<br />[http://www.noncode.org/ NONCODE, Tsinghua University and Chinese Academy of Sciences, Beijing, China]
    BDGP Single Nucleotide Polymorphism (SNP) Project:
+
* <b>Rfam</b>, A collection of RNA sequence families of structural RNAs including non-coding RNA genes as well as cis-regulatory elements (last updated 2017):<br />[http://rfam.xfam.org/ Rfam, EMBL-EBI, Hinxton, UK]
    »Berkeley Drosophila Genome Project, University of California, Berkeley, USA
+
* <b>RNAcentral</b>, Integrated access to a comprehensive and up-to-date set of non-coding RNA sequences provided by a collaborating group of Expert Databases (last updated 2017):<br />[http://rnacentral.org/ RNAcentral, EMBL-EBI, Hinxton, UK]
    Berkeley Drosophila Genome Project (BDGP):
+
 
    »BDGP, University of California, Berkeley, USA
+
==lncRNA==
    BDTNP, ChIP/chip in vivo DNA binding data:
+
* <b>lncrnadb</b>, Long Noncoding RNA Database (last updated 2015):<br />[http://www.lncrnadb.org/ lncrnadb, University of New South Wales, Sydney, Australia]
    »Berkeley Drosophila Transcription Network Project, University of California, Berkeley, USA
+
* <b>LNCediting</b>, Function of RNA editing in lncRNAs (last updated 2016):<br />[http://bioinfo.life.hust.edu.cn/LNCediting/fly/ LNCediting, Huazhong University of Science and Technology, Wuhan, China and University of Texas, Houston, Texas, USA]
    CluSTr protein sequence similarity analysis of Drosophila:
+
 
    »CluSTr proteome analysis, EBI, UK
+
==miRNA==
    D. pseudoobscura genome project:
+
===General===
    »Human Genome Sequencing Center, Baylor College of Medicine, USA
+
* <b>miRBase</b>, A searchable database of published miRNA sequences and annotations (last updated 2014):<br />[http://www.mirbase.org/ miRBase, University of Manchester, UK]<br />
    D. simulans genome project:
+
::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.
    »Genome Sequencing Center, Washington University, USA
+
* <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]
    D. yakuba genome project:
+
* <b>Tools4miRs</b>, Manually curated platform gathering methods for the broadly-defined miRNA analysis (last updated 2017):<br />[https://tools4mirs.org/ Tools4miRs, Polish Academy of Sciences and University of Warsaw, Warsaw, Poland]
    »Genome Sequencing Center, Washington University, USA
+
* <b>TransmiR</b>, A database of transcription factor-microRNA regulation (last updated 2013):<br />[http://www.cuilab.cn/transmir TransmiR, Peking University Health Science Center, Peking, Chin
    D.melanogaster UCSC Genome Browser Gateway:
+
 
    »University of California, Santa Cruz, USA
+
===miRNA Target Prediction===
    DDBJ, the DNA Data Bank of Japan:
+
* <b>DIANA microT-CDS</b>, MicroRNA Target Prediction (last updated 2014):<br />[http://diana.imis.athena-innovation.gr/DianaTools/index.php?r=microT_CDS/index DIANA microT-CDS, DIANA LAB, Athens, Greece]
    »DDBJ, National Institute of Genetics, Mishima, Japan
+
* <b>MicroCosm Targets</b>, Computationally predicted targets for microRNAs across many species based on MiRanda algorithm (last updated 2007):<br />[http://didattica.cribi.unipd.it/genomica/Genomics_2013/9-mirna/Microcosm%20Targets.html MicroCosm Targets, EMBL-EBI, Hinxton, UK]
    DNase I Footprint Database:
+
* <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]
    »University of Manchester Bioinformatics Resources, University of Manchester, UK
+
* <b>miRNA_Targets</b> (last updated 2011):<br />[http://mamsap.it.deakin.edu.au/~amitkuma/mirna_targetsnew/index.html miRNA targets on full length mRNAs, Deakin University, Victoria, Australia]
    Drosophila Heterochromatin Genome Project (DHGP):
+
* <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]
    »DHGP, Lawrence Berkeley National Laboratory, USA
+
* <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]
    Drosophila melanogaster Exon Database (DEDB):
+
 
    »DEDB, National University of Singapore
+
===Validated miRNA Targets===
    Drosophila Polymorphism Database:
+
* <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]
    »Drosophila Polymorphism Database, Univ. Autònoma de Barcelona, Spain
+
* <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]
    Drosophila Population Genomic Project (DPGP):
+
* <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]
    »DPGP, University of California, Davis, USA
+
 
    Drosophila simulans and yakuba sequencing projects:
+
===Comparative miRNA Analysis===
    »DPGP, University of California, Davis, USA
+
* <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]
    Drosophilidae Taxonomic Database:
+
* <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]
    »Drosophilidae Taxonomic Database, Japan
+
* <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]
    Drosophilidae Taxonomy - Collection of Papers:
+
 
    »Japan Drosophila Database (JDD) on Taxonomy, Japan
+
==rRNA==
    DRSC, Drosophila RNAi Screening Center:
+
* <b>SILVA</b>, High quality ribosomal RNA databases (last updated 2016):<br />[https://www.arb-silva.de/ SILVA, Max Planck Institute for Marine Microbiology and Jacobs University, Bremen, Germany]
    »DRSC, Harvard Medical School, Boston, MA, USA
+
 
    EMBL Nucleotide Sequence Database:
+
==tRNA==
    »EMBL Nucleotide Sequence Database, EBI, Cambridge, UK
+
* <b>GtRNAdb</b>, tRNAscan-SE analysis of complete genomes:<br />[http://gtrnadb.ucsc.edu/ GtRNAdb, Lowe lab, University of California, Santa Cruz, Santa Cruz, CA, USA]
    EPD, the Eukaryotic Promoter Database:
+
* <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]
    »EPD, Epalinges s/Lausanne, Switzerland
+
 
    euGenes, Genomic Information for Eukaryotic Organisms, including Drosophila:
+
==snoRNA==
    » euGenes, Indiana University, USA
+
* <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 ]
    EvoPrinter, Identification of Evolutionarily Resilient DNA Sequences
+
==SRP RNA==
    »NINDS, NIH, Bethesda MD, USA
+
* <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]
    FLIGHT, Fly database for the Integration of Genomic and High-Throughput data:
+
 
    »FLIGHT Database, Ludwig Institute for Cancer Research, London, UK
+
=Ontology Resources=
    FlyAtlas, the Drosophila adult gene expression atlas:
+
* <b>AmiGO 2</b>, tools for searching and browsing the Gene Ontology database:<br />[http://amigo2.berkeleybop.org/amigo AmiGO 2, Berkeley Bioinformatics Open-source Projects, USA]
    »FlyAtlas, University of Glasgow, UK
+
* <b>BioPortal</b>, a biomedical ontologies repository and browser:<br />[http://bioportal.bioontology.org/ BioPortal, The National Center for Biomedical Ontology, USA]
    FlyMine, an integrated database for Drosophila & Anopheles genomics:
+
* <b>Disease Ontology</b>, ontology of disease terms:<br />[http://disease-ontology.org/ Disease Ontology]
    »University of Cambridge, United Kingdom
+
* <b>Gene Ontology Consortium</b><br />[http://geneontology.org/ Gene Ontology Consortium]
    FlyPhenomics, phenotypic differences between species of the D. melanogaster subgroup:
+
* <b>GOrilla</b> -- Gene Ontology enRIchment and anaLysis and viuaLizAtion tool:<br />[http://cbl-gorilla.cs.technion.ac.il/ GOrilla, Israel]
    »FlyPhenomics, Paris, France
+
* <b>OboEdit</b>, browser for OBO ontologies:<br />[http://oboedit.org/ OboEdit]
    FlySNP Project:
+
* <b>The OBO Foundry</b>, an ontology registry:<br />[http://obofoundry.github.io/ OboFoundry]
    »FlySNP, Austrian Academy of Sciences, Austria
+
* <b>Ontobee</b>, an ontologies browser:<br />[http://www.ontobee.org/ Ontobee, He Group, University of Michigan Medical School, Ann Arbor, Michigan, USA]
    GenBank,the NIH genetic sequence database:
+
* <b>Ontology Lookup Service</b>, an ontologies browser:<br />[http://www.ebi.ac.uk/ontology-lookup/ Ontology Lookup Service, EMBL-EBI, Hinxton, UK]
    »GenBank, NCBI, Bethesda, MD USA
+
* <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]
    GenomeRNAi, Heidelberg, a database of RNA interference (RNAi) screens in cultured Drosophila cells:
+
* <b>QuickGO</b>, a browser for Gene Ontology terms and annotations:<br />[http://www.ebi.ac.uk/QuickGO/ QuickGO, EMBL-EBI, Hinxton, UK]
    »GenomeRNAi, DKFZ, Heidelberg, Germany
+
 
    GEO, NCBI's Gene Expression Omnibus:
+
=Orthology Predictions=
    »GEO, NCBI, Bethesda, MD USA
+
* <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]
    GPCRDB, information system for G protein-coupled receptors (GPCRs):
+
* <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]
    »GPCRDB, The GPCRDB (G Protein-Coupled Receptor Data Base) partnership
+
* <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]
    Homophila, Human Disease to Drosophila Gene Database:
+
* <b>EggNOG</b>, A database of orthologous groups and functional annotation:<br />[http://eggnogdb.embl.de/#/app/home Computational Biology Group, EMBL, Heidelberg, Germany]
    » Homophila, San Diego, 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]
    InParanoid, Eukaryotic Ortholog Groups:
+
* <b>Inparanoid</b>, InParanoid: ortholog groups with inparalogs<br />[http://inparanoid.sbc.su.se/cgi-bin/index.cgi Stockholm Bioinformatics Centre, Stockholm, Sweden]
    »InParanoid, Karolinska Institute, 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]
    InterPro protein domain analysis of Drosophila:
+
* <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]
    »InterPro proteome analysis, EBI, UK
+
* <b>OrthoDB</b>, The Hierarchical Catalog of Orthologs<br />[http://orthodb.org/ Zdobnov Computational Evolutionary Genomics group, University of Geneva, Geneva, Switzerland]
    MANTiS a phylogenetic framework for multi-species genome comparisons:
+
* <b>OrthoMCL</b>, Ortholog Groups of Protein Sequences<br />[http://www.orthomcl.org/orthomcl/ EuPathDB]
    »MANTiS, Université Libre de Bruxelles, Belgium
+
* <b>PANTHER</b>, PANTHER Classification System<br />[http://pantherdb.org/genes/ Thomas Lab, University of Southern California, Los Angeles, CA, USA]
    MEROPS, an information resource for peptidases:
+
* <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]
    »MEROPS, The Sanger Institute, Cambridge, UK
+
* <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]
    miRBase, microRNA data:
+
* <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]
    »miRBase, The Sanger Institute, Cambridge, UK
+
 
    miRNA, Target Gene Prediction:
+
=Phylogenetic Comparison Tools=
    »miRNA - Target Prediction, EMBL, Heidelberg, Germany
+
* <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]
    MitoDrome, Drosophila melanogaster nuclear genes encoding for mitochondrial proteins:
+
* <b>EvoPrinter</b>, Identification of Evolutionarily Resilient DNA Sequences<br />[http://evoprinter.ninds.nih.gov/ NINDS, NIH, Bethesda MD, USA]
    »MitoDrome, Bari, Italy
+
* <b>HomoloGene</b> -- automated system fo constructing putative homology groups:<br />[http://www.ncbi.nlm.nih.gov/homologene NCBI, Bethesda, MA, USA]
    Mitotic Spindle Assembly Database:
+
* <b>InParanoid</b>, Eukaryotic Ortholog Groups:<br />[http://inparanoid.sbc.su.se/cgi-bin/index.cgi InParanoid, Karolinska Institute, Sweden]
    »Genes Required for Mitotic Spindle Assembly in S2 cells, University of California, San Francisco, USA
+
* <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]
    NHGRI Drosophila Genome Sequencing Proposals, Status of Sequencing:
+
* <b>OrthoDB</b>, the Hierarchical Catalog of Orthologs:<br />[http://www.orthodb.org/ OrthoDB, University of Geneva, Switzerland]
    »National Human Genome Research Institute, Bethesda, MD, USA
+
* <b>flyDIVaS</b>, a comparative genomics database resource of ''Drosophila'' divergence and selection: <br />[http://flydivas.info/ Temple University, Philadelphia, PA, USA]
    Panther protein classification system:
+
* <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]
    »Panther Protein Classification System, Applied Biosystems & Celera, USA
+
 
    PDB, Protein Data Bank:
+
=Population Biology and Polymorphism Resources=
    »PDB, The Research Collaboratory for Structural Bioinformatics (RCSB) consortium
+
* <b>BDGP Single Nucleotide Polymorphism (SNP) Project</b>:<br />[http://www.fruitfly.org/SNP/ Berkeley Drosophila Genome Project, University of California, Berkeley, USA]
    PhospoPep - phosphorylation site data from D. melanogaster cell lines:
+
* <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]
    »The Aebersold group at the ETH in collaboration with the FGCZ in Switzerland, and the ISB, 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]
    Proteome analysis of Drosophila:
+
* <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]
    »Proteome analysis, EBI, UK
+
* <b>Drosophila Polymorphism Database</b>:<br />[http://dpdb.uab.es/dpdb/dpdb.asp DPDB, Universitat Autonoma de Barcelona, Barcelona, Spain]
    PubMed, Biomedical literature citations and abstracts:
+
* <b>DPGP</b>, Drosophila Population Genomics Project:<br />[http://www.dpgp.org/ DPGP, University of California, Davis, USA]
    »PubMed, NCBI, Bethesda, MD USA
+
* <b>DSPR</b>, Drosophila Synthetic Population Resource:<br />[http://wfitch.bio.uci.edu/~dspr/index.html DSPR, University of Kansas and UC Irvine, USA]* <b>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]
    REDfly, Regulatory Element Database for Drosophila:
+
* <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]
    »REDfly, University at Buffalo, New York, USA
+
 
    Rfam, RNA families database of alignments and CMs:
+
=Protein Analysis=
    »Rfam, the Sanger Institute, Cambridge, UK and Janelia Farm, Ashburn, VA, USA
+
* <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]
    Sebida, Sex Bias Database:
+
* <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]
    »Sebida, MPI Martinsried, Germany
+
* <b>InterPro</b> protein domain analysis of Drosophila:<br />[http://www.ebi.ac.uk/interpro/ InterPro: protein sequence analysis & classification, EBI, UK]
    TaxoDros, the database on Taxonomy of Drosophilidae:
+
* <b>MEROPS</b>, an information resource for peptidases:<br />[http://merops.sanger.ac.uk/ MEROPS, Wellcome Trust Sanger Institute, Hinxton, UK]
    »TaxoDros, University of Zurich, Switzerland
+
* <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]
    The Drosophila Transcription Factor Database:
+
* <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]
    »FlyTF.org, MRC Cambridge, UK
+
* <b>PDB</b>, Protein Data Bank:<br />[http://www.rcsb.org/pdb/home/home.do PDB, The Research Collaboratory for Structural Bioinformatics (RCSB) consortium]
    The McGill Drosophila melanogaster Genome Project:
+
* <b>PhospoPep</b>, interactive interrogation of MS-derived phosphorylation data from 4 different organisms: <br />[http://www.phosphopep.org/index.php Institute for Systems Biology, Seattle, Washington, USA]
    »McGill Drosophila Genome Project, Canada
+
* <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]
    TRANSFAC, A database of transcription factors and their binding sites:
+
* <b>RBPDB</b>, the database of RNA-binding protein specificities:<br />[http://rbpdb.ccbr.utoronto.ca/ RBPDB]
    »TRANSFAC, Braunschweig, Germany
+
* <b>SMART</b>, Simple Modular Architecture Research Tool:<br />[http://smart.embl-heidelberg.de/ SMART, Protein Domain Analysis, EMBL, Heidleberg]
    TransTerm, a Translational Signal Database:
+
* <b>UniProtKB</b>, a comprehensive catalog of information on proteins:<br />[https://www.uniprot.org/uniprot/ UniProtKB, The UniProt Consortium]
    »TransTerm, Dunedin, New Zealand
+
 
    UniProtKB, a comprehensive catalog of information on proteins:
+
=Public Education=
    »UniProtKB, The UniProt Consortium
+
* <b>About the history of Drosophila research</b>, An extensive collection of media pertaining to the history of fruit fly research: <br />[http://www.flyfacility.ls.manchester.ac.uk/forthepublic/outreachresources/#History Manchester Fly Facility, University of Manchester, UK]
    Whole genome comparative analysis of D. melanogaster and D. pseudoobscura:
+
* <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]
    »Whole genome analysis, LBNL, USA
+
* <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>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>Manchester Fly Facility Public Resource Page</b>:<br />[http://www.flyfacility.ls.manchester.ac.uk/forthepublic/ 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 hits in DRSC screens</b>:<br /> [http://www.flyrnai.org/RNAi_find_hit_info.html DRSC-TRiP-FGR, Harvard Medical School, Boston, MA, USA]
 +
* <b>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>Tsinghua Fly Center</b>, Transgenic RNAi lines: <br />[http://center.biomed.tsinghua.edu.cn/public/eq-category/modelanimalfacility/ Center of Biomedical Analysis, Tsinghua University, Beijing, China]
 +
* <b>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=
 +
* <b>DCPD</b> -- Drosophila Core Promoter Database, A list of 205 Drosophila melanogaster core promoters aligned by their empirically determined transcription start site: <br />[http://labs.biology.ucsd.edu/Kadonaga/DCPD.htm Kadonaga Lab, UCSD, San Diego, California, USA]
 +
* <b>EvoPrinterHD</b>, A "High Definition" view of conserved DNA: <br />[http://evoprinter.ninds.nih.gov/evoprintprogramHD/drosophila.html NINDS, NIH, Bethesda, MD, USA]
 +
* <b>FlyPrimerBank</b>, a comprehensive qPCR primer database for Drosophila: <br />[http://www.flyrnai.org/FlyPrimerBank FlyPrimerBank, DRSC, Harvard Medical School, Boston, MA, USA]
 +
* <b>FGENESH</b>, Annotation of animal genomes-genes, promoters, functional motifs, protein sub-cellular localization.:<br />[http://www.softberry.com/berry.phtml?topic=case_study_animal&no_menu=on Annotation of genomes, Softberry, USA]
 +
* <b>GenePalette</b>, a tool for genome sequence visualization and navigation: <br />[http://www.genepalette.org/ GenePalette, University of California, San Diego, USA]
 +
* <b>Genie Gene finder for Drosophila</b>:<br />[http://www.fruitfly.org/seq_tools/genie.html Genie, Berkeley Drosophila Genome Project, University of California, Berkeley, USA]
 +
* <b>HRMA</b> -- High Resolution Melt Analysis: <br /> [http://www.flyrnai.org/hrma HRMA, DRSC, Harvard Medical School, Boston, MA, 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]
 +
* <b>RepeatMasker</b>: <br />[http://www.repeatmasker.org/ RepeatMasker Institute for Systems Biology, Seattle, WA, USA]
 +
* <b>Splice Site Prediction for Drosophila</b>:<br />[http://www.fruitfly.org/seq_tools/splice.html Splice Site Prediction, Berkeley Drosophila Genome Project, University of California, Berkeley, USA]
 +
* <b>Web Apollo</b>, a collaborative genomic annotation editor: <br />[http://apollo.berkeleybop.org/ Web Apollo, LBL, Berkeley, USA]
 +
 
 +
=Taxonomy=
 +
* <b>Drosophilidae Taxonomic Database</b>:<br />[http://bioinfo.lowtem.hokudai.ac.jp/db/modules/stdb/ Drosophilidae Taxonomic Database, Japan]
 +
* <b>Drosophilidae Taxonomy</b> -- Collection of Papers:<br />[http://www.dgrc.kit.ac.jp/~jdd/class/index.html Japan Drosophila Database (JDD) on Taxonomy, Japan]
 +
* <b>FlyPhenomics</b>, phenotypic differences between species of the ''D. melanogaster'' subgroup:<br />[http://www.normalesup.org/~vorgogoz/FlyPhenomics/ FlyPhenomics, Paris, France]
 +
* <b>TaxoDros</b>, the database on Taxonomy of Drosophilidae:<br />[http://www.taxodros.uzh.ch/ TaxoDros, University of Zurich, Switzerland]
 +
* <b>Taxonomy</b>, NCBI Taxonomy Database:<br />[http://www.ncbi.nlm.nih.gov/taxonomy NCBI, Bethesda, MD USA]
 +
 
 +
=Transcription Regulation Databases and Tools=
 +
* <b>BDTNP</b>, ChIP/chip in vivo DNA binding data:<br />[http://bdtnp.lbl.gov:8080/Fly-Net/ Berkeley Drosophila Transcription Network Project, University of California, Berkeley, 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>DBD</b>, Transcription factor prediction database: <br />[http://www.transcriptionfactor.org/index.cgi?Home DBD, MRC, Cambridge, UK]
 +
* <b>ElemeNT</b>, An interactive tool for rapid and convenient detection of core promoter elements within a given sequence, implemented in Perl programming language: <br />[http://lifefaculty.biu.ac.il/gershon-tamar/index.php/element-description Juven-Gershon Lab, Bar-Ilan University, Ramat-Gan, Israel]
 +
 
 +
* <b>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 Specificitiies: <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>i-cisTarget</b>, An integrative genomics method for the prediction of regulatory features and cis-regulatory modules in Human, Mouse, and Fly:<br />[http://gbiomed.kuleuven.be/apps/lcb/i-cisTarget/ i-cisTarget, University of Leuven, Leuven, Belgium]
 +
* <b>Neural Network Promoter Prediction for Drosophila</b>:<br />[http://www.fruitfly.org/seq_tools/promoter.html Neural Network Promoter Prediction, Berkeley Drosophila Genome Project, University of California, Berkeley, USA]
 +
* <b>OnTheFly</b>, Database of Drosophila Transcription Factors and Transcription Factor Binding Sites <br />[https://bhapp.c2b2.columbia.edu/OnTheFly/index.php OnTheFly, Columbia University, USA]
 +
* <b>REDfly</b>, Regulatory Element Database for Drosophila:<br />[http://redfly.ccr.buffalo.edu/ REDfly, University at Buffalo, New York, USA]
 +
* <b>The Drosophila Transcription Factor Database</b>:<br />[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]
 +
 
 +
=Suggest a tool or resource=
 +
*Please [http://flybase.org/contact/email contact Flybase] to suggest a tool or resource for the list.
 +
 
 +
[[Category:DONE]]

Latest revision as of 03:59, 29 March 2019

Atlases, Images and Videos

CRISPRs and TALENs

Data Repositories

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

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

Public Education

RNAi

Sequence Analysis

Taxonomy

Transcription Regulation Databases and Tools

Suggest a tool or resource