Difference between revisions of "FlyBase:Drosophila Online Resources"

From FlyBase Wiki
Jump to navigation Jump to search
(Created page with "=Model Organisms= {| class="wikitable" border="1" |- ! Database ! Organism ! Organism (Genus and species) |- | [http://hymenopteragenome.org/beebase/ BeeBase] | Honey Bee | ...")
 
 
(651 intermediate revisions by 11 users not shown)
Line 1: Line 1:
=Model Organisms=
+
=Atlases, Images and Videos=
{| class="wikitable" border="1"
+
* <b>Atlas of Drosophila Development</b>, An Atlas following the main events of embryogenesis and post-embryonic development:<br />[http://www.sdbonline.org/sites/fly/atlas/00atlas.htm Volker Hartenstein and Interactive Fly, Bethesda, MD, USA]
|-
+
* <b>CSIRO</b> Anatomical Atlas of Flies:<br />[http://www.ento.csiro.au/biology/fly/fly.html# CSIRO Entomology, Australia]
! Database
+
* <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]
! Organism
+
* <b>FlyCircuit</b>, a Database of Drosophila Brain Neurons:<br />[http://www.flycircuit.tw/ FlyCircuit, National Tsing Hua University, Taiwan]
! Organism (Genus and species)
+
* <b>FlyMove</b>, an Image, Movie and Interactive Shockwave Resource:<br />[http://flymove.uni-muenster.de/ FlyMove, Muenster, Germany]
|-
+
* <b>FlyPNS</b>, ''D. melanogaster'' embryonic and larval peripheral nervous system:<br />[http://www.normalesup.org/~vorgogoz/FlyPNS/page1.html FlyPNS, UMPC, Paris, France and Columbia University, NY, USA]
| [http://hymenopteragenome.org/beebase/ BeeBase]  
+
* <b>FlyView</b>, a Drosophila Image Database:<br />[http://flyview.uni-muenster.de/ FlyView, Muenster, Germany]
| Honey Bee
+
* <b>GETDB</b>, a Gal4 enhancer trap database:<br />[https://kyotofly.kit.jp/stocks/GETDB/getdb.html GETDB, Kyoto Institute of Technology, Kyoto, Japan]
| Apis mellifera
+
* <b>Jove</b>, videos of experimental techniques:<br />[http://www.jove.com/index/browse.stp?Search=Drosophila Jove, Journal of Visualized Experiments, USA]
|-
+
* <b>PeptideAtlas</b>, a multi-organism, publicly accessible compendium of peptides identified in a large set of tandem mass spectrometry proteomics experiments: <br />[http://www.peptideatlas.org/ Seattle Proteome Center, Seattle, Washington, USA]
| [http://beetlebase.org/ BeetleBase]
+
* <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]
| Red Flour Beetle
 
| Tribolium castaneum
 
|-
 
| [http://dictybase.org/ DictyBase]
 
| Soil Amoeba
 
| Dictyostelium discoideum
 
|-
 
| [http://ecocyc.org/ EcoCyc]
 
| Bacteria
 
| Escherichia coli
 
|-
 
| [http://www.gramene.org/ Gramene]
 
| Grasses
 
|
 
|-
 
| [http://www.informatics.jax.org/ MGI]
 
| Mouse
 
| Mus musculus
 
|-
 
| [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=OMIM/ OMIM]
 
| Human
 
| Homo sapiens
 
|-
 
| [http://www.yeastgenome.org// SGD]
 
| Budding Yeast
 
| Saccharomyces cerevisiae
 
|-
 
| [http://www.genedb.org/genedb/pombe/index.jsp S. pombe GeneDB]
 
| Fission Yeast
 
| Schizosaccharomyces pombe
 
|-
 
| [http://www.arabidopsis.org/ TAIR]
 
| Mouse-ear cress
 
| Arabidopsis thaliana
 
|-
 
| [http://www.vectorbase.org/index.php VectorBase]
 
| Mosquitos and Deer Tick
 
| Anopheles gambiae, Aedes aegypti, Culex pipiens quinquefasciatus, Ixodes scapularis
 
|-
 
| [http://www.wormbase.org/ WormBase]
 
| Round worms
 
| Caenorhabditis
 
|-
 
| [http://zfin.org/cgi-bin/webdriver?MIval=aa-ZDB_home.apg ZFIN]
 
| Zebrafish
 
| Danio rerio
 
|}
 
  
=Related Projects=
+
=Cell Lines and Cell Culture=
:[http://www.gmod.org/ GMOD]
+
* <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]
:[http://www.geneontology.org/ Gene Ontology (GO)]
+
* <b>DGRC: Cell Line Catalog</b>: <br /> [https://dgrc.bio.indiana.edu/ Drosophila Genomics Resource Center, Indiana University, Bloomington, IN, USA]
:[http://www.genomeknowledge.org/ Reactome]
+
* <b>DGRC: Cell Culture Protocols</b>: <br />[https://dgrc.bio.indiana.edu/Protocols?tab=cells Drosophila Genomics Resource Center, Indiana University,  Bloomington, IN, USA]
:[http://www.fruitfly.org/ BDGP (Berkeley Drosophila Genome Project)]
+
* <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]
:[http://dgrc.cgb.indiana.edu/ DGRC (Drosophila Genomics Resource Center)]
+
* <b>DGRC: Feeder Cells</b>: <br />[https://dgrc.bio.indiana.edu/cells/FeederCells Drosophila Genomics Resource Center, Indiana University, Bloomington, IN, USA]
:[http://www.ou.edu/journals/dis/byissue.html DIS by issue]
+
* <b>DGRC: Fly Extract</b>:<br />[https://dgrc.bio.indiana.edu/cells/FlyExtract Drosophila Genomics Resource Center, Indiana University, Bloomington, IN, USA]
:[http://www.flyexpress.net/ FlyExpress]
+
* <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]
:[http://www.sdbonline.org/fly/aimain/1aahome.htm Interactive Fly]
+
* <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]
:[http://www.modencode.org/ modENCODE]
+
* <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]
:[http://www.textpresso.org/fly/ Textpresso for Fly]
 
  
=Stock Collections=
+
=CRISPRs and TALENs=
===''D. melanogaster'' Collections===
+
* <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]
:[http://flystocks.bio.indiana.edu/ Bloomington]
+
* <b>CCTop</b> CRISPR/Cas9 optimum target finder:<br />[http://crispr.cos.uni-heidelberg.de/ Center for Organismal Studies, Heidelberg University, Heidelberg, DE]
:[http://www.drosdel.org.uk/ DrosDel]
+
* <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]
:[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 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.dgrc.kit.ac.jp/ Kyoto]
+
* <b>CRISPR Guide Design Resources</b> CRISPR Design Tool:<br />[https://zlab.bio/guide-design-resources  Zhang Lab, MIT, Boston, MA, USA]
:[http://www.shigen.nig.ac.jp/fly/nigfly/ NIG-Fly]
+
* <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]
:[http://stockcenter.vdrc.at/control/main VDRC]
+
* <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>, Overview: <br />[https://flycrispr.org/ O'Connor-Giles, Wildonger, and Harrison Labs, University of Wisconsin-Madison, WI, USA]
 +
* <b>flyCRISPR</b>, Target Finder:<br />[https://flycrispr.org/target-finder// O'Connor-Giles Lab, University of Wisconsin-Madison, WI, USA]
 +
* <b>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>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]
  
===Species Collections===
+
=Data Repositories=
:[http://kyotofly.kit.jp/cgi-bin/ehime/index.cgi Ehime]
+
* <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 />[https://flypush.research.bcm.edu/pscreen/index.php GDP, Baylor College of Medicine, Texas]<br />[https://flypush.research.bcm.edu/pscreen/transposons.html Schematic drawings of Transposons]
 +
* <b>GenBank</b>,the NIH genetic sequence database:<br />[http://www.ncbi.nlm.nih.gov/Genbank/ GenBank, NCBI, Bethesda, 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===
+
=DNA Reagents=
:'''Drosophila Gene Search Project'''
+
* <b>Addgene Highly requested Drosophila plasmids</b>: <br />[https://www.addgene.org/search/catalog/pooled-libraries/?q=Drosophila Addgene, Watertown, MA, USA]
:Information about ordering P{GS} lines can be found at http://gsdb.biol.metro-u.ac.jp/~dclust/index.html
+
* <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]
  
:'''Ehime Drosophila Species Stock Center of Japan'''
+
=Drosophila Genomes Data and Metadata=
: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>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]]
  
:'''FlyTrap Stock Collection'''
+
=Gene Expression Databases and Tools=
:GFP protein trap lines from the FlyTrap project can be obtained at Yale University, USA at http://flytrap.med.yale.edu/
+
* <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>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]
  
:'''FlyView Stock Collection'''
+
=Gene Groups=
:Enhancer trap lines from the FlyView project can be obtained at University of Muenster, Germany at http://flyview.uni-muenster.de/
+
* <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]
  
:'''Kyorin-Fly'''
+
=General Bioinformatics Tools=
: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>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>GSEA</b>, Gene Set Enrichment Analysis:<br />[http://www.broadinstitute.org/gsea/index.jsp GSEA, Broad Institute, Cambridge, MA, USA]
  
:'''Tübingen Drosophila Stock Collection'''
+
=Genome Sequencing Projects=
:A list of approximately 2,000 Drosophila stocks at the Max-Planck-Institute for Developmental Biology.
+
* <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]
  
:'''UC San Diego Drosophila Stock Center'''
+
=Human Disease: Drosophila Models and Orthologous Genes=
:Approximately 270 different Drosophila species at University of San Diego, USA can be obtained at https://stockcenter.ucsd.edu/info/welcome.php
+
* <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>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.]
  
:'''University of Cambridge FlyProt project'''
+
=Interaction and Pathway Databases=
: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>BioCyc - FLY</b> -- Curated Drosophila melanogaster Pathways:<br />[http://biocyc.org/FLY/organism-summary?object=FLY FlyCyc, Harvard University, Cambridge, USA]
 +
* <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>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>SignaLink</b>, an integrated resource to analyze signaling pathway cross-talks, transcription factors, miRNAs and regulatory enzymes.:<br />[http://signalink.org/ SignaLink, Earlham Institute, Norwich, UK]
 +
* <b>STRING</b>, Known and Predicted Protein-Protein Interactions<br />[http://string-db.org/ STRING, SIB, Switzerland CPR, Denmark, and EMBL, Heidelberg, Germany]
 +
* <b>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]
  
=Vectors and Constructs=
+
=Metabolomics=
http://flybase.org/static_pages/lists/vectors.html
+
* <b>FlyMet</b>, A Tissue- and Sex-Specific Metabolomic Atlas and Database :<br />[http://www.flymet.org/ FlyMet, University of Glasgow, Glasgow, Scotland]
  
=Listing of all resources=
+
=Miscellaneous=
==Drosophila Network Resources==
+
* <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]
===Comparative Analyses and Genome Databases===
+
* <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://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>Drosophila Workers Unite! A laboratory manual for working with Drosophila</b>:<br />[https://marksteinlab.org/dwu/ Michele Markstein Lab, UMass Amherst, Amherst, MA, USA]
 +
* <b>The Encyclopedia of North American Drosophilids Volume 1: Drosophilids of the Midwest and Northeast</b>:<br />[https://digitalcommons.mtu.edu/oabooks/1/ by T. Werner, Michigan Technological University, Tessa Steenwinkel, Michigan Technological University, and J.Jaenike, University of Rochester]
 +
* <b>Fly Art</b> - A compendium of arty imagery, sculptures or poetry inspired by Drosophila or flies in the wider sense.:<br />[https://droso4public.wordpress.com/fly-art/ University of Manchester, Manchester, UK]
 +
* <b>Fly 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>GlyCosmos Portal</b>, a Web portal aiming to integrate the glycosciences with the life sciences. It consists of Standards, Repositories and Data Resources, providing information about genes, proteins, lipids, pathways and diseases.:<br />[https://glycosmos.org/ GlyCosmos, GlyCosmos is a member of the GlySpace Alliance, consisting of ExPASy Glycomics, GlyCosmos, and GlyGen]
 +
* <b>Interactive Fly</b>, A cyberspace guide to Drosophila development and metazoan evolution<br />[http://www.sdbonline.org/fly/aimain/1aahome.htm Interactive Fly, Bethesda, MD, USA]
 +
* <b>J*fly</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>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]
  
    Assembly/Alignment/Annotation of 12 related Drosophila species:
+
=Non-coding (ncRNA) Databases and Tools=
    »Assembly/Alignment/Annotation, LBNL, USA
+
 
    BDGP Single Nucleotide Polymorphism (SNP) Project:
+
==General==
    »Berkeley Drosophila Genome Project, University of California, Berkeley, USA
+
* <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]
    Berkeley Drosophila Genome Project (BDGP):
+
* <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]
    »BDGP, 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 :<br />[http://rnacentral.org/ RNAcentral, EMBL-EBI, Hinxton, UK]
    BDTNP, ChIP/chip in vivo DNA binding data:
+
 
    »Berkeley Drosophila Transcription Network Project, University of California, Berkeley, USA
+
==lncRNA==
    CluSTr protein sequence similarity analysis of Drosophila:
+
* <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]
    »CluSTr proteome analysis, EBI, UK
+
* <b>LncRBase</b>, a database of information about lncRNAs from 8 species (human, mouse, fly, zebrafish, rat, chicken, C.elegans and cow) :<br />[http://bicresources.jcbose.ac.in/zhumur/lncrbase/ LncRBase, Bose Institute, West Bengal, India]
    D. pseudoobscura genome project:
+
 
    »Human Genome Sequencing Center, Baylor College of Medicine, USA
+
==miRNA==
    D. simulans genome project:
+
===General===
    »Genome Sequencing Center, Washington University, USA
+
* <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 />
    D. yakuba 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.melanogaster UCSC Genome Browser Gateway:
+
* <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]
    »University of California, Santa Cruz, USA
+
* <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
    DDBJ, the DNA Data Bank of Japan:
+
 
    »DDBJ, National Institute of Genetics, Mishima, Japan
+
===miRNA Target Prediction===
    DNase I Footprint Database:
+
* <b>DIANA microT-CDS</b>, MicroRNA Target Prediction:<br />[https://dianalab.e-ce.uth.gr/html/dianauniverse/index.php?r=microT_CDS DIANA Tools, DIANA LAB, Athens, Greece]
    »University of Manchester Bioinformatics Resources, University of Manchester, UK
+
* <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]
    Drosophila Heterochromatin Genome Project (DHGP):
+
* <b>miRWalk - The Database on Predicted and Validated microRNA Targets</b> :<br />[http://mirwalk.umm.uni-heidelberg.de/ 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 />[https://dianalab.e-ce.uth.gr/html/diana/web/index.php?r=tarbasev8 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>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:
+
 
    »Drosophilidae Taxonomic Database, Japan
+
==rRNA==
    Drosophilidae Taxonomy - Collection of Papers:
+
* <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]
    »Japan Drosophila Database (JDD) on Taxonomy, Japan
+
 
    DRSC, Drosophila RNAi Screening Center:
+
==tRNA==
    »DRSC, Harvard Medical School, Boston, MA, 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]
    EMBL Nucleotide Sequence Database:
+
 
    »EMBL Nucleotide Sequence Database, EBI, Cambridge, UK
+
==snoRNA==
    EPD, the Eukaryotic Promoter Database:
+
* <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 ]
    »EPD, Epalinges s/Lausanne, Switzerland
+
==SRP RNA==
    euGenes, Genomic Information for Eukaryotic Organisms, including Drosophila:
+
* <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]
    » euGenes, Indiana University, USA
+
 
    EvoPrinter, Identification of Evolutionarily Resilient DNA Sequences
+
=Ontology Resources=
    »NINDS, NIH, Bethesda MD, USA
+
* <b>BioPortal</b>, a biomedical ontologies repository and browser:<br />[http://bioportal.bioontology.org/ BioPortal, The National Center for Biomedical Ontology, USA]
    FLIGHT, Fly database for the Integration of Genomic and High-Throughput data:
+
* <b>Disease Ontology (DO)</b>, ontology of disease terms:<br />[http://disease-ontology.org/ Disease Ontology]
    »FLIGHT Database, Ludwig Institute for Cancer Research, London, UK
+
* <b>Gene Ontology Consortium (GO)</b><br />[http://geneontology.org/ Gene Ontology Consortium]
    FlyAtlas, the Drosophila adult gene expression atlas:
+
* <b>GOrilla</b> -- Gene Ontology enRIchment and anaLysis and viuaLizAtion tool:<br />[http://cbl-gorilla.cs.technion.ac.il/ GOrilla, Israel]
    »FlyAtlas, University of Glasgow, UK
+
* <b>OboEdit</b>, browser for OBO ontologies:<br />[http://oboedit.org/ OboEdit]
    FlyMine, an integrated database for Drosophila & Anopheles genomics:
+
* <b>The OBO Foundry</b>, an ontology registry:<br />[http://obofoundry.github.io/ OboFoundry]
    »University of Cambridge, United Kingdom
+
* <b>Ontobee</b>, an ontologies browser:<br />[http://www.ontobee.org/ Ontobee, He Group, University of Michigan Medical School, Ann Arbor, Michigan, USA]
    FlyPhenomics, phenotypic differences between species of the D. melanogaster subgroup:
+
* <b>Ontology Lookup Service</b>, an ontologies browser:<br />[http://www.ebi.ac.uk/ontology-lookup/ Ontology Lookup Service, EMBL-EBI, Hinxton, UK]
    »FlyPhenomics, Paris, France
+
* <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]
    FlySNP Project:
+
* <b>QuickGO</b>, a browser for Gene Ontology terms and annotations:<br />[http://www.ebi.ac.uk/QuickGO/ QuickGO, EMBL-EBI, Hinxton, UK]
    »FlySNP, Austrian Academy of Sciences, Austria
+
 
    GenBank,the NIH genetic sequence database:
+
=Orthology Predictions=
    »GenBank, 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]
    GenomeRNAi, Heidelberg, a database of RNA interference (RNAi) screens in cultured Drosophila cells:
+
* <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]
    »GenomeRNAi, DKFZ, Heidelberg, Germany
+
* <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]
    GEO, NCBI's Gene Expression Omnibus:
+
* <b>EggNOG</b>, A database of orthologous groups and functional annotation:<br />[http://eggnogdb.embl.de/#/app/home Computational Biology Group, EMBL, Heidelberg, Germany]
    »GEO, NCBI, Bethesda, MD USA
+
* <b>Gene2Function</b>:<br /> [http://www.gene2function.org/search/ Gene2Function, Harvard Medical School, Boston, MA, USA]
    GPCRDB, information system for G protein-coupled receptors (GPCRs):
+
* <b>Hieranoid</b>, Hieranoid: an orthology inference method using a hierarchical approach. Hieranoid performs pairwise orthology analysis using InParanoid at each node in a guide tree as it progresses from its leaves to the root.<br />[https://hieranoid.sbc.su.se/index.html Stockholm Bioinformatics Centre, Stockholm, Sweden]
    »GPCRDB, The GPCRDB (G Protein-Coupled Receptor Data Base) partnership
+
* <b>HieranoidDB</b>, HieranoidDB: An online database of Hieranoid orthologs.<br />[https://hieranoidb.sbc.su.se/ Stockholm Bioinformatics Centre, Stockholm, Sweden]
    Homophila, Human Disease to Drosophila Gene Database:
+
* <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]
    » Homophila, San Diego, USA
+
* <b>Inparanoid</b>, InParanoid: ortholog groups with inparalogs<br />[http://inparanoid.sbc.su.se/cgi-bin/index.cgi Stockholm Bioinformatics Centre, Stockholm, Sweden]
    InParanoid, Eukaryotic Ortholog Groups:
+
* <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]
    »InParanoid, Karolinska Institute, Sweden
+
* <b>MARRVEL</b>, Model organism Aggregated Resources for Rare Variant ExpLoration:<br />[http://marrvel.org/ MARRVEL, Baylor College of Medecine, Houston, TX, 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 />[https://www.orthodb.org/ Zdobnov Computational Evolutionary Genomics group, University of Geneva, Geneva, Switzerland]
    MANTiS a phylogenetic framework for multi-species genome comparisons:
+
* <b>OrthoFinder</b>, A comprehensive platform for comparative genomics that finds orthogroups and orthologs, infers rooted gene trees for all orthogroups and identifies all of the gene duplication events.<br />[http://www.stevekellylab.com/software/orthofinder University of Oxford, Oxford, UK]
    »MANTiS, Université Libre de Bruxelles, Belgium
+
* <b>OrthoInspector</b>, A software suite for inference of orthologous relationships between protein coding-genes and an online resource to access and query precomputed orthology databases.<br />[https://lbgi.fr/orthoinspectorv3/ ICube Laboratory, Graffenstaden, France]
    MEROPS, an information resource for peptidases:
+
* <b>OrthoMCL</b>, Ortholog Groups of Protein Sequences<br />[http://www.orthomcl.org/orthomcl/ EuPathDB]
    »MEROPS, The Sanger Institute, Cambridge, UK
+
* <b>PANTHER</b>, PANTHER Classification System<br />[http://pantherdb.org/genes/ Thomas Lab, University of Southern California, Los Angeles, CA, USA]
    miRBase, microRNA data:
+
* <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]
    »miRBase, 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]
    miRNA, Target Gene Prediction:
+
* <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]
    »miRNA - Target Prediction, EMBL, Heidelberg, Germany
+
 
    MitoDrome, Drosophila melanogaster nuclear genes encoding for mitochondrial proteins:
+
=Phylogenetic Comparison Tools=
    »MitoDrome, Bari, Italy
+
* <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]
    Mitotic Spindle Assembly Database:
+
* <b>HomoloGene</b> -- automated system fo constructing putative homology groups:<br />[http://www.ncbi.nlm.nih.gov/homologene NCBI, Bethesda, MA, USA]
    »Genes Required for Mitotic Spindle Assembly in S2 cells, University of California, San Francisco, USA
+
* <b>InParanoid</b>, Eukaryotic Ortholog Groups:<br />[http://inparanoid.sbc.su.se/cgi-bin/index.cgi InParanoid, Karolinska Institute, Sweden]
    NHGRI Drosophila Genome Sequencing Proposals, Status of Sequencing:
+
* <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]
    »National Human Genome Research Institute, Bethesda, MD, USA
+
* <b>OrthoDB</b>, the Hierarchical Catalog of Orthologs:<br />[http://www.orthodb.org/ OrthoDB, University of Geneva, Switzerland]
    Panther protein classification system:
+
* <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]
    »Panther Protein Classification System, Applied Biosystems & Celera, 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]
    PDB, Protein Data Bank:
+
 
    »PDB, The Research Collaboratory for Structural Bioinformatics (RCSB) consortium
+
=Population Biology and Polymorphism Resources=
    PhospoPep - phosphorylation site data from D. melanogaster cell lines:
+
* <b>BDGP Single Nucleotide Polymorphism (SNP) Project</b>:<br />[http://www.fruitfly.org/SNP/ Berkeley Drosophila Genome Project, University of California, Berkeley, USA]
    »The Aebersold group at the ETH in collaboration with the FGCZ in Switzerland, and the ISB, 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]
    Proteome analysis of Drosophila:
+
* <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, EBI, UK
+
* <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]
    PubMed, Biomedical literature citations and abstracts:
+
* <b>Drosophila Polymorphism Database</b>:<br />[http://dpdb.uab.es/dpdb/dpdb.asp DPDB, Universitat Autonoma de Barcelona, Barcelona, Spain]
    »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]
    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 and Modification=
    »Rfam, the Sanger Institute, Cambridge, UK and Janelia Farm, Ashburn, VA, USA
+
* <b>AlphaFold Protein Structure Database</b>, AlphaFold DB provides open access to protein structure predictions; An AI system developed by DeepMind that predicts a protein’s 3D structure from its amino acid sequence:<br />[https://alphafold.ebi.ac.uk/ EMBL-EBI, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK]
    Sebida, Sex Bias Database:
+
* <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, MPI Martinsried, Germany
+
* <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]
    TaxoDros, the database on Taxonomy of Drosophilidae:
+
* <b>InterPro</b> protein domain analysis of Drosophila:<br />[http://www.ebi.ac.uk/interpro/ InterPro: protein sequence analysis & classification, EBI, UK]
    »TaxoDros, University of Zurich, Switzerland
+
* <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]
    The Drosophila Transcription Factor Database:
+
* <b>LARKSdb</b>, a tool to predict regions of proteins that may be involved in reversible amyloid formation and phase-separation based on protein structure predictions:<br />[https://srv.mbi.ucla.edu/LARKSdb/index.py/ LARKSdb, UCLA, Los Angeles, CA, USA]
    »FlyTF.org, MRC Cambridge, UK
+
* <b>MEROPS</b>, an information resource for peptidases:<br />[http://merops.sanger.ac.uk/ MEROPS, Wellcome Trust Sanger Institute, Hinxton, UK]
    The McGill Drosophila melanogaster Genome Project:
+
* <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]
    »McGill Drosophila Genome Project, Canada
+
* <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]
    TRANSFAC, A database of transcription factors and their binding sites:
+
* <b>PDB</b>, Protein Data Bank:<br />[http://www.rcsb.org/pdb/home/home.do PDB, The Research Collaboratory for Structural Bioinformatics (RCSB) consortium]
    »TRANSFAC, Braunschweig, Germany
+
* <b>PhospoPep</b>, Protein Phosphorylation Database: <br />[http://www.phosphopep.org/index.php Institute for Systems Biology, Seattle, Washington, USA]
    TransTerm, a Translational Signal Database:
+
* <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]
    »TransTerm, Dunedin, New Zealand
+
* <b>RBPDB</b>, the database of RNA-binding protein specificities:<br />[http://rbpdb.ccbr.utoronto.ca/ RBPDB]
    UniProtKB, a comprehensive catalog of information on proteins:
+
* <b>SMART</b>, Simple Modular Architecture Research Tool:<br />[http://smart.embl-heidelberg.de/ SMART, Protein Domain Analysis, EMBL, Heidleberg]
    »UniProtKB, The UniProt Consortium
+
* <b>UniProtKB</b>, a comprehensive catalog of information on proteins:<br />[https://www.uniprot.org/uniprot/ UniProtKB, The UniProt Consortium]
    Whole genome comparative analysis of D. melanogaster and D. pseudoobscura:
+
 
    »Whole genome analysis, LBNL, USA
+
=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=
 +
* <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>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]
 +
 
 +
=Single Cell RNA-seq=
 +
* <b>ASAP</b> Automated Single-cell Analysis Pipeline: <br />[https://asap.epfl.ch/ ASAP, EPFL, Lausanne, Switzerland, Swiss Institute of Bioinformatics, Lausanne, Switzerland]
 +
 
 +
* <b>cisTopic</b> Probabilistic modelling of cis-regulatory topics from single cell epigenomics data: <br />[https://github.com/aertslab/cisTopic/ cisTopic, VIB Center for Brain & Disease Research, Leuven, Belgium, Department of Human Genetics, KU Leuven, Leuven, Belgium]
 +
 
 +
* <b>DeepCMC</b> A Neural Networks (NN) based approach for identifying genes that contain spatial information: <br />[https://github.com/TJU-CMC-Org/SingleCell-DREAM DeepCMC, Thomas Jefferson University, Philadelphia, PA, USA]
 +
 
 +
* <b>Distmap</b> To spatially map single cell RNA sequencing data by using an existing reference database of in situs: <br />[https://github.com/rajewsky-lab/distmap Distmap, BIMSB and MDC, Berlin, Germany]
 +
 
 +
* <b>DRscDB</b> DRSC scRNA-seq DataBase: <br />[https://www.flyrnai.org/tools/single_cell/ DRscDB, DRSC, Harvard Medical School, Boston, USA]
 +
 
 +
* <b>DVEX</b> Drosophila Virtual Expression eXplorer: <br />[https://shiny.mdc-berlin.de/DVEX/ DVEX, BIMSB and MDC, Berlin, Germany]
 +
 
 +
* <b>Fly Cell Atlas</b> A consortium of Drosophila researchers interested in single-cell genomics, transcriptomics, and epigenomics: <br />[https://flycellatlas.org/ Fly Cell Atlas, Founders - Stein Aerts, Leuven, Belgium, Bart Deplancke, Lausanne, Switzerland, Robert Zinzen, Berlin, Germany]
 +
 
 +
* <b>Lasso.TopX</b> An approach using the Lasso and ranking statistics for identifying genes that contain spatial information: <br />[https://github.com/TJU-CMC-Org/SingleCell-DREAM/ Lasso.TopX, Thomas Jefferson University, Philadelphia, PA, USA]
 +
 
 +
* <b>novoSpaRc</b> Predicts locations of single cells in space by solely using single-cell RNA sequencing data.: <br />[https://github.com/rajewsky-lab/novosparc novoSpaRc, Harvard and Broad Institute, Cambridge, MA, USA, Max Delbrück Center, Berlin, Germany]
 +
 
 +
* <b>SCEA</b> Single Cell Expression Atlas - Single Cell Gene Expression Across Species: <br />[https://www.ebi.ac.uk/gxa/sc SCEA, EMBL-EBI, Hinxton, UK, Sanger Institute, Wellcome Genome Campus, Hinxton, UK, Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK]
 +
 
 +
* <b>SCENIC</b> Single-Cell Regulatory Network Inference and Clustering <br />[https://github.com/aertslab/SCENIC SCENIC, Center for Brain & Disease Research, Leuven, Belgium, KU Leuven, Leuven, Belgium, University of Liege, Liege, Belgium, VIB Center for Cancer Biology, Leuven, Belgium]
 +
 
 +
* <b>SCope</b> Fast Visualization Tool for Large-Scale and High Dimensional Single-Cell Data <br />[https://github.com/aertslab/SCope SCope, VIB KU Leuven, Leuven, Belgium]
 +
 
 +
* <b>Seurat</b> An R package designed for QC, analysis, and exploration of single-cell RNA-seq data.: <br />[https://satijalab.org/seurat/ Seurat, NYU, NY, NY, USA]
 +
 
 +
* <b>VSN</b> A Repository of Pipelines for Single-Cell Data Analysis in Nextflow DSL2:  <br />[https://github.com/vib-singlecell-nf/vsn-pipelines VSN-Pipelines]
 +
 
 +
=Taxonomy=
 +
* <b>Taxonomy of Drosophilidae</b> -- Collection of Papers:<br />[http://www.drosophila.jp/jdd/index_en.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> Drosophilidae Taxonomic Database:<br />[https://bioinfo.museum.hokudai.ac.jp/ Drosophilidae Taxonomic Database, Japan]
 +
* <b>TaxoDros</b>, the database on Taxonomy of Drosophilidae:<br />[http://www.taxodros.uzh.ch/ TaxoDros, University of Zurich, Switzerland]
 +
* <b>Taxonomy</b>, NCBI Taxonomy Database:<br />[http://www.ncbi.nlm.nih.gov/taxonomy NCBI, Bethesda, MD USA]
 +
 
 +
=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>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 - retired<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>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>ReMap</b>, a large-scale integrative analysis of DNA-binding experiments for Homo sapiens, Mus musculus, Dropshiphila melanogaster, and Arabadopsis thaliana transcriptional regulators based on manual curation of ChIP-seq, ChIP-exo, DAP-seq from public sources:<br />[https://remap.univ-amu.fr/ ReMap, TAGC Inserm, Marseille, France]
 +
* <b>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>scEnhancer</b>, A database of single cell enhancer annotation in human, mouse, and fly:<br />[http://enhanceratlas.net/scenhancer/ scEnhancer, Sun Yat-sen University, Shenzhen, China and Johns Hopkins University, Baltimore, MD, USA]
 +
* <b>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]]

Latest revision as of 17:05, 1 September 2022

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

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