External Drosophila Resources

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Drosophila Network Resources
Comparative Analyses and Genome Databases
	Assembly/Alignment/Annotation of 12 related Drosophila species: »Assembly/Alignment/Annotation, LBNL, USA BDGP Single Nucleotide Polymorphism (SNP) Project: »Berkeley Drosophila Genome Project, University of California, Berkeley, USA Berkeley Drosophila Genome Project (BDGP): »BDGP, University of California, Berkeley, USA BDTNP, ChIP/chip in vivo DNA binding data: »Berkeley Drosophila Transcription Network Project, University of California, Berkeley, USA CluSTr protein sequence similarity analysis of Drosophila: »CluSTr proteome analysis, EBI, UK D. pseudoobscura genome project: »Human Genome Sequencing Center, Baylor College of Medicine, USA D. simulans genome project: »Genome Sequencing Center, Washington University, USA D. yakuba genome project: »Genome Sequencing Center, Washington University, USA D.melanogaster UCSC Genome Browser Gateway: »University of California, Santa Cruz, USA DDBJ, the DNA Data Bank of Japan: »DDBJ, National Institute of Genetics, Mishima, Japan DNase I Footprint Database: »University of Manchester Bioinformatics Resources, University of Manchester, UK Drosophila Heterochromatin Genome Project (DHGP): »DHGP, Lawrence Berkeley National Laboratory, USA Drosophila melanogaster Exon Database (DEDB): »DEDB, National University of Singapore Drosophila Polymorphism Database: »Drosophila Polymorphism Database, Univ. Autònoma de Barcelona, Spain Drosophila Population Genomic Project (DPGP): »DPGP, University of California, Davis, USA Drosophila simulans and yakuba sequencing projects: »DPGP, University of California, Davis, USA Drosophilidae Taxonomic Database: »Drosophilidae Taxonomic Database, Japan Drosophilidae Taxonomy - Collection of Papers: »Japan Drosophila Database (JDD) on Taxonomy, Japan DRSC, Drosophila RNAi Screening Center: »DRSC, Harvard Medical School, Boston, MA, USA EMBL Nucleotide Sequence Database: »EMBL Nucleotide Sequence Database, EBI, Cambridge, UK EPD, the Eukaryotic Promoter Database: »EPD, Epalinges s/Lausanne, Switzerland euGenes, Genomic Information for Eukaryotic Organisms, including Drosophila: » euGenes, Indiana University, USA EvoPrinter, Identification of Evolutionarily Resilient DNA Sequences »NINDS, NIH, Bethesda MD, USA FLIGHT, Fly database for the Integration of Genomic and High-Throughput data: »FLIGHT Database, Ludwig Institute for Cancer Research, London, UK FlyAtlas, the Drosophila adult gene expression atlas: »FlyAtlas, University of Glasgow, UK FlyMine, an integrated database for Drosophila & Anopheles genomics: »University of Cambridge, United Kingdom FlySNP Project: »FlySNP, Austrian Academy of Sciences, Austria GenBank,the NIH genetic sequence database: »GenBank, NCBI, Bethesda, MD USA GenomeRNAi, Heidelberg, a database of RNA interference (RNAi) screens in cultured Drosophila cells: »GenomeRNAi, DKFZ, Heidelberg, Germany GEO, NCBI's Gene Expression Omnibus: »GEO, NCBI, Bethesda, MD USA GPCRDB, information system for G protein-coupled receptors (GPCRs): »GPCRDB, The GPCRDB (G Protein-Coupled Receptor Data Base) partnership Homophila, Human Disease to Drosophila Gene Database: » Homophila, San Diego, USA InParanoid, Eukaryotic Ortholog Groups: »InParanoid, Karolinska Institute, Sweden InterPro protein domain analysis of Drosophila: »InterPro proteome analysis, EBI, UK MANTiS a phylogenetic framework for multi-species genome comparisons: »MANTiS, Université Libre de Bruxelles, Belgium MEROPS, an information resource for peptidases: »MEROPS, The Sanger Institute, Cambridge, UK miRBase, microRNA data: »miRBase, The Sanger Institute, Cambridge, UK miRNA, Target Gene Prediction: »miRNA - Target Prediction, EMBL, Heidelberg, Germany MitoDrome, Drosophila melanogaster nuclear genes encoding for mitochondrial proteins: »MitoDrome, Bari, Italy Mitotic Spindle Assembly Database: »Genes Required for Mitotic Spindle Assembly in S2 cells, University of California, San Francisco, USA NHGRI Drosophila Genome Sequencing Proposals, Status of Sequencing: »National Human Genome Research Institute, Bethesda, MD, USA Panther protein classification system: »Panther Protein Classification System, Applied Biosystems & Celera, USA PDB, Protein Data Bank: »PDB, The Research Collaboratory for Structural Bioinformatics (RCSB) consortium PhospoPep - phosphorylation site data from D. melanogaster cell lines: »The Aebersold group at the ETH in collaboration with the FGCZ in Switzerland, and the ISB, USA. Proteome analysis of Drosophila: »Proteome analysis, EBI, UK PubMed, Biomedical literature citations and abstracts: »PubMed, NCBI, Bethesda, MD USA REDfly, Regulatory Element Database for Drosophila: »REDfly, University at Buffalo, New York, USA Rfam, RNA families database of alignments and CMs: »Rfam, the Sanger Institute, Cambridge, UK and Janelia Farm, Ashburn, VA, USA Sebida, Sex Bias Database: »Sebida, MPI Martinsried, Germany TaxoDros, the database on Taxonomy of Drosophilidae: »TaxoDros, University of Zurich, Switzerland The Drosophila Transcription Factor Database: »FlyTF.org, MRC Cambridge, UK The McGill Drosophila melanogaster Genome Project: »McGill Drosophila Genome Project, Canada TRANSFAC, A database of transcription factors and their binding sites: »TRANSFAC, Braunschweig, Germany TransTerm, a Translational Signal Database: »TransTerm, Dunedin, New Zealand UniProtKB, a comprehensive catalog of information on proteins: »UniProtKB, The UniProt Consortium Whole genome comparative analysis of D. melanogaster and D. pseudoobscura: »Whole genome analysis, LBNL, USA
Sequence Traces of Drosophila Genomes
	D. ananassae genomic sequence trace archives: »NCBI Trace Archives, USA »Ensembl FTP Trace Repository, EBI, UK D. erecta genomic sequence trace archives: »NCBI Trace Archives, USA »Ensembl FTP Trace Repository, EBI, UK D. grimshawi genomic sequence trace archives: »NCBI Trace Archives, USA »Ensembl FTP Trace Repository, EBI, UK D. melanogaster genomic sequence trace archives: »NCBI Trace Archives, USA »Ensembl FTP Trace Repository, EBI, UK D. mojavensis genomic sequence trace archives: »NCBI Trace Archives, USA »Ensembl FTP Trace Repository, EBI, UK D. persimilis genomic sequence trace archives: »NCBI Trace Archives, USA »Ensembl FTP Trace Repository, EBI, UK D. pseudoobscura genomic sequence trace archives: »NCBI Trace Archives, USA »Ensembl FTP Trace Repository, EBI, UK D. sechellia genomic sequence trace archives: »NCBI Trace Archives, USA »Ensembl FTP Trace Repository, EBI, UK D. simulans genomic sequence trace archives: »NCBI Trace Archives, USA »Ensembl FTP Trace Repository, EBI, UK D. virilis genomic sequence trace archives: »NCBI Trace Archives, USA »Ensembl FTP Trace Repository, EBI, UK D. willistoni genomic sequence trace archives: »NCBI Trace Archives, USA »Ensembl FTP Trace Repository, EBI, UK D. yakuba genomic sequence trace archives: »NCBI Trace Archives, USA »Ensembl FTP Trace Repository, EBI, UK
Genetic and Protein Interaction Databases
	BioGRID, The General Repository for Interaction Datasets »BioGRID, Mount Sinai Hospital, Toronto, Canada DroID, Drosophila Interactions Database »Drosophila Interaction Database, Detroit, USA Drosophila PIMRider, Drosophila Protein Interaction Map »Drosophila PIMRider, Hybrigenics, Paris, France Flynet, Drosophila Protein-protein Interactions »Flynet, Johns Hopkins University, Baltimore, MD, USA IM Browser, Drosophila Interactions Database »IM Browser, Wayne State University, Detroit, MI, USA
Sequence Analysis
	cis-analyst, to search the Drosophila genome for clusters of binding sites: »cis-analyst, USA Gene-Finder for Drosophila: »Gene Finding, FGENESH, SoftBerry GenePalette, a tool for genome sequence visualization and navigation: »GenePalette, University of California, San Diego, USA Genie Gene finder for Drosophila: »Genie, USA Neural Network Promoter Prediction for Drosophila: »Neural Network Promoter Prediction, USA PREdictor, to identify Polycomb/Trithorax response elements: »PREdictor, Bielefeld University, Germany Splice Site Prediction for Drosophila: »Splice Site Prediction, USA Stubb site, to find clusters of cis-regulatory binding sites: »Stubb web site, Rockefeller University, New York, USA Target Explorer, to identify clusters of transcription factor binding sites: »Target Explorer, Columbia University, New York, USA
Atlases, Images and Videos
	BDTNP, A cellular resolution 3D gene expression and morphology Atlas of the blastoderm. »BDTNP, University of California, Berkeley, USA CSIRO Entomology Anatomical Atlas of Flies: »CSIRO Entomology, Australia Electron micrograph maps of Drosophila melanogaster polytene chromosomes: »Sorsa Maps, Helsinki, Finland Fly Motor Axon Page: »Motor Axon, California Institute of Technology, USA FlyBrain, an Online Atlas and Database of the Drosophila Nervous System: »FlyBrain, University of Freiburg, Freiburg, Germany »FlyBrain, University of Arizona, Tucson, USA FlyEx, a Database of Segmentation Gene Expression in Drosophila: »FlyEx, St. Petersburg State Polytechnical University, Russia »FlyEx, Stony Brook University, USA FlyExpress, an Expression Pattern Search Engine: »FlyExpress, Arizona State University, USA FlyMove, an Image, Movie and Interactive Shockwave Resource: »FlyMove, Muenster, Germany FlyTrap, a GFP Protein Trap Database: »FlyTrap, Yale University, USA flytrap, a database of P{GAL4} enhancer traps and their expression in brains: »flytrap, University of Edinburgh, UK FlyView, a Drosophila Image Database: »FlyView, Muenster, Germany GETDB, a Gal4 enhancer trap database: »GETDB, National Institute of Basic Biology, Okazaki, Japan Jove, videos of experimental techniques: »Jove, Journal of Visualized Experiments, USA Patterns of gene expression in Drosophila embryogenesis: »Gene expression database, BDGP, USA Scans of Bridges' original 1935 polytene drawings for D. melanogaster: »GEM Website, University of Hawaii, USA
Miscellaneous
	Drosophila Information Service: »DIS, Norman, Oklahoma, USA FlyNome, a database of Drosophila nomenclature: »FlyNome, USA FlyPNS, embryonic and larval peripheral nervous system: »FlyPNS, USA Interactive Fly, A cyberspace guide to Drosophila development and metazoan evolution »Interactive Fly, Bethesda, MD, USA Jfly , a data depository for the fly and other insects, with an emphasis for the Japanese-speaking fly community: »Jfly, University of Tokyo, Japan The WWW Virtual Library--Drosophila: »Drosophila Virtual Library Tracheal Database, information on tracheal development in Drosophila: »Tracheal Database, Switzerland

Drosophila Material Resources
Genomic Clones
Bac Genomic Clones and Filters
	Only one BAC clone library is now available, made from DNA of the same y¹ ; cn¹ bw¹ sp¹ stock as was used for the Berkeley Drosophila Genome Project P1 clones. This BACR library was made for the BDGP by K. Osoegawa, A. Mammoser, and P. de Jong. BACR clones (18,432 clones in pBACe3.6; average clone size is 160-Kb) are available from BACPAC Resources at: http://bacpac.chori.org/dromel98.htm
P1 Genomic Clones
	As the P1 library is largely obsolete, the BDGP is discouraging the use of P1 clones. If there is a compelling scientific reason that a corresponding BAC is not sufficient, requests for P1 clones can be directed to the BDGP. For additional information about the Berkeley Drosophila Genome Project see http://www.fruitfly.org.
Cosmid Genomic Clones and Filters
	EDGP cosmids are available from the Geneservice: http://www.geneservice.co.uk/products/clones/drosophila.jsp. Cosmids are available either singly or on high-density filters. The members of the European Drosophila Genome mapping consortium are: F.C. Kafatos, C. Louis, C. Savakis, I. Siden-Kiamos. Institute of Molecular Biology and Biotechnology, FORTH, Heraklion, Crete. D.M. Glover and R.D.C. Saunders, Department of Biochemistry, University of Dundee, Dundee, Scotland. M. Ashburner, Department of Genetics, University of Cambridge, Cambridge, England. J. Modolell, Centro de Biologia Molecular, Universidad Autonoma, Madrid, Spain. Supported by the Stimulation Action Programme of the European Community, with initial funding from the Fondation Schlumberger.
YAC Genomic Clones
	A complete set of YAC clones is maintained by Ian Duncan and clones may be requested from him. Contact: Ian W. Duncan, Department of Biology, Box 1137, Washington University, St. Louis, MO 63130-4899. Telephone (1)-314-935-6719; fax(1)-314-935-4432; e-mail duncan@biology.wustl.edu.
Sibling Species Genomic Libraries
	Fosmid Libraries from BACPAC Resources Genomic fosmid libraries were constructed for the BDGP by Andreas Gnirke at Exelixis, Inc. (South San Francisco) from Drosophila erecta, D. pseudoobscura, D. virilis, and D. willistoni. The fosmid libraries are available from BACPAC Resources at: http://bacpac.chori.org/drosofosmid.htm
cDNA (EST) Clones and Libraries
	Addgene Addgene helps labs archive and share their plasmids that have appeared in publications. http://www.addgene.org/pgvec1?f=c&cmd=browse Berkeley Drosophila Genome Project The information is provided by BDGP. If you don't find the information you need here check http://www.fruitfly.org/about/materials/ for possible updates. Brian Oliver Laboratory Testis cDNA clones and filters constructed by Justen Andrews in Brian Oliver's laboratory at the NIH are available from the Geneservice in the UK. Ordering information can be found at http://www.geneservice.co.uk/products/cdna/dros_cdna.jsp cDNA library aliquots Aliquots from a number of the BDGP cDNA libraries are available from the labs on this list. Clontech Clontech (BD Biosciences) offers D.melanogaster embryo and larva 5'-STRETCH cDNA libraries at http://www.clontech.com/products/cat/HTML/1186.shtml Drosophila Gene Collection (DGC) Contact BACPAC Resources, Open Biosystems, Geneservice, or the DGRC for clones in DGCr1.0 or DGCr2.0. Drosophila Genomics Resource Center (DGRC) Collects and distributes DNA clones, including vectors, cDNAs, and ESTs. More information is available at http://dgrc.cgb.indiana.edu/ EST Project cDNA Clones Contact the DGRC for cDNA clones from the BDGP EST collection.
Arrays and Primers
	Affymetrix The Affymetrix GeneChip Drosophila Genome Array for gene expression analysis based on Release 3.1 annotations can be obtained at http://www.affymetrix.com/products/arrays/specific/fly_2.affx The Affymetrix Drosophila Tiling 2.0R Array based on Genome Release 5 with comprehensive genome coverage at 38bp resolution can be obtained here: http://www.affymetrix.com/products/arrays/specific/drosophila_tiling2_0r.affx Drosophila Genomics Resource Center (DGRC) Produces and distributes DNA microarray slides. More information is available at http://dgrc.cgb.indiana.edu/ FlyChip FlyChip is a publicly funded project to provide a non-profit microarray resource for the UK Drosophila research community. More information is available at http://www.flychip.org.uk/ International Drosophila Array Consortium (INDAC) An international consortium to collaborate in the development and aquisition of microarray resources for the benefit of the entire research community. More information is available at http://www.indac.net/ UK Drosophila Affymetrix Microarray Service A publicly funded microarray service for the UK Drosophila research community. More information is available at http://www.mblab.gla.ac.uk/igf/
Stocks
	BDGP/Baylor Gene Disruption Project Information about ordering P{GT1}(BG), P{SuporP}(KG), and P{Epgy2}(EY) lines from Baylor College of Medicine, Texas, USA can be found at http://flypush.imgen.bcm.tmc.edu/pscreen/ Bloomington Stock Center A large collection of stocks at Indiana Univerisity, USA can be obtained at http://flystocks.bio.indiana.edu DrosDel Project Information about ordering isogenic deficiency lines at the University of Cambridge, UK can be found at http://www.drosdel.org.uk/ Drosophila Gene Search Project Information about ordering P{GS} lines can be found at http://gsdb.biol.metro-u.ac.jp/~dclust/index.html Ehime Drosophila Species Stock Center of Japan 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/ Exelixis Collection at Harvard Medical School Information about ordering the Exelixis stocks at Harvard Medical School can be found at http://drosophila.med.harvard.edu/ FlyTrap Stock Collection GFP protein trap lines from the FlyTrap project can be obtained at Yale University, USA at http://flytrap.med.yale.edu/ FlyView Stock Collection Enhancer trap lines from the FlyView project can be obtained at University of Muenster, Germany at http://flyview.uni-muenster.de/ GETDB--Gal4 Enhancer Trap Insertion Database Information about ordering Gal4 enhancer trap lines generated and analyzed by NP Consortium from the Drosophila Genetic Resource Center in Kyoto, Japan can be found at http://flymap.lab.nig.ac.jp/~dclust/getdb.html Japanese Laboratories Stock lists from individual laboratories in Japan are available at http://www.grs.nig.ac.jp/fly/CENTER.e.html Kyoto Stock Center Information about ordering P element insertion lines, deficiency, or duplication kits at the Kyoto Institute of Technology, Japan can be found at http://www.dgrc.kit.ac.jp/en/index.html NIG-FLY: Fly Stocks of the National Institute of Genetics Stocks for RNA interference experiments may be obtained from the NIG RNAi fly unit at http://www.shigen.nig.ac.jp/fly/nigfly/ Szeged Stock Centre Information about ordering P{lacW}, P{EP}, P{RS3}, and P{RS5} insertion lines at the University of Szeged, Hungary can be obtained at http://expbio.bio.u-szeged.hu/fly/index.php Tübingen Drosophila Stock Collection A list of approximately 2,000 Drosophila stocks at the Max-Planck-Institute for Developmental Biology. Tucson Stock Center Approximately 270 different Drosophila species at University of Arizona, USA can be obtained at http://stockcenter.arl.arizona.edu Vienna Drosophila RNAi Center Stocks for RNA interference experiments can be obtained from the IMP, Austria at http://stockcenter.vdrc.at/control/main
Expression Vectors
	Drosophila Gateway Vectors A set of 68 Gateway-based vectors designed to express epitope-tagged proteins in Drosophila culture cells or flies, available at the DGRC
Cell Lines and Hybridomas
	ATCC The American Type Culture Collection (ATCC) provides Schneider's L-2 and L-2/M delta 2-3 cell lines and hybridomas at http://www.atcc.org/catalog/cellBiology/cellBiologyIndex.cfm Developmental Studies Hybridoma Bank The Developmental Studies Hybridoma Bank at the University of Iowa offers hybridomas and antibodies at http://dshb.biology.uiowa.edu Drosophila Genomics Resource Center (DGRC) Collects and distributes cell lines. More information is available at http://dgrc.cgb.indiana.edu/
Antibodies
	Clontech Cocalico Biologicals Developmental Studies Hybridoma Bank Novagen Sigma-Aldrich US Biological
RNA
	Clontech Clontech of BD Biosciences offers adult, embryo, and larva Poly A+ RNA at http://www.clontech.com/products/detail.asp?product_id=167106&tabno=2
RNAi
	Drosophila RNAi Screening Center The Drosophila RNAi screening center at Harvard Medical School provides high throughput RNAi screens. More information is available at http://flyrnai.org/RNAi_index.html Geneservice Geneservice, in collaboration with Cyclacel Limited, offers a collection of 13,600 RNAi constructs in its Drosophila genome RNAi library. More information is available at http://www.geneservice.co.uk/products/rnai/Dros_RNAi.jsp Open Biosystems Open Biosystems provides the Drosophila RNAi Collection version 1.0, a collection of dsDNA constructs for generation of dsRNA, at http://www.openbiosystems.com/RNAi/DrosophilaRNAicollections/
Transgenic, Targeted Mutation, and Other Services
	Aktogen behaviour genetic services Aktogen at Cambridge University offers a wide range of services to the fruit fly community such as behaviour tests, behaviour and other equipment, custom made genetic constructs and transgenic services. http://www.aktogen.com/ BestGene Transgenic Service The BestGene Drosophila Embryo Injection service provides partial to full service ranging from DNA preparation, embryo microinjection to balancing crosses. More information is available at http://www.thebestgene.com/ Drosophila TILLING Project The goal of Fly-TILL is to rapidly deliver to the Drosophila community EMS-induced mutations in requested genes via high-throughput reverse genetic screens. More information is available at http://tilling.fhcrc.org:9366/fly/ Duke University Non-Mammalian Model Systems Flyshop The Duke University Non-Mammalian Model Systems Flyshop provides P-element transformation, dsRNA injection, embryo sorting, and inverse PCR services. More information is available at http://www.biology.duke.edu/model-system Fly Facility Fly Facility located at the Universite d'Auvergne Clermont-Ferrand I, France, provides a transgenesis and dsRNA microinjection service. More information is available at http://www.fly-facility.com/ Genetic Services Genetic Services provides the Drosophila community with services including transgenic production, injection work, genetic screening, stock creation, construct production and consulting. More information is available at http://www.geneticservices.com GenetiCorps Custom Injection Services GenetiCorps offers high quality fly injection services to the Drosophila research community. For more information, please visit http://www.geneticorps.com/ Genetivision, Inc. Genetivision offers a transgenic fly service for both delta 2-3 transposase-mediated P-element transgenesis and Phi-C31 mediated site-specific integration. More information is available at http://www.genetivision.com/ Model Biosystems Drosophila Stock Center The stock center in Bangalore offers a stock maintenance service at a very reasonable price to the Drosophila researchers all over the world http://www.modelbiosystems.com Rainbow Transgenic Flies Rainbow Transgenic Flies provides professional microinjection services to the fly community. More information is available at http://www.rainbowgene.com/ Transgenic Drosophila Fly Core The Cutaneous Biology Research Center (CRBC) Fly Core at Massachusetts General Hospital/Harvard Medical School provides microinjection services to create transgenic Drosophila fly strains. More information is available at http://www.flycore.com Union Biometrica COPAS Select flow cytometry instruments are able to analyze and dispense Drosophila embryos on the basis of size and fluorescent signals. More information is available at http://www.unionbio.com/ VANEDIS Drosophila injection service The VANEDIS Drosophila injection service injects embryos with your construct of interest. More information is available at http://www.vanedis.no