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 Drosophila

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Databases / searches:
    • FlyBase is the primary Drosophila database integrating genetic and molecular data on Drosophila genes, alleles, transcripts and proteins, as well as stocks, genomic clones, bibliographic information and much more...
    • DGRC -- Drosophila Genomics Resource Center: collects and distributes DNA vectors, cDNAs, ESTs, cell lines, microarrays etc. 
    • InteractiveFly  "A cyberspace guide to Drosophila genes and their roles in development"
    • Two hybrid interaction map of the Drosophila Proteome. CuraGen Corporation, in collaboration with researchers at The Johns Hopkins University, Wayne State University School of Medicine and Yale University School of Medicine, completed the world's first comprehensive protein interaction map for a multicellular organism, Drosophila melanogaster, and published the results in the online edition and the December 5, 2003 print edition of Science.
    • AAA - The Assembly/Alignment/Annotation of 12 Drosophila Genomes
  • Genome Projects:
    • BDGP As part of the integration of FlyBase services, the Gadfly annotation database and Berkeley Fly BLAST have been retired. Equivalent services are now available from the FlyBase server at Indiana University.
    • Drosophila melanogaster @ NCBI. The assembled and annotated genome sequence of the euchromatic arms of the five D. melanogaster chromosomes available in GenBank.
    • DHGP Drosophila Heterochromatin Genome Project
    • DRSC Drosophila RNAi Screening Center.
    • EDGP  The European Drosophila Genome Project.
    • McGill Drosophila Genome Project was originally launched to generate genetic and molecular data from the 37-38 polytene region. This interval contains approximately 1.8Mb of sequence. Now it covers region 37-40.
    • AAA - The Assembly/Alignment/Annotation of 12 Drosophila Genomes
  • Drosophila-specific search and analysis at various Databases:
    • FlyBase: All Searches.
    • BDGP Analysis Tools. 
    • BLAST:
      • BLAST at NCBI (Basic Local Alignment Search Tool) is a set of similarity search programs designed to explore all of the available sequence databases regardless of whether the query is protein or DNA. Almost any BLAST search at NCBI can be limited to Drosophila sequences.
      • Fly BLAST at FlyBase  The BLAST programs were tailored for sequence similarity searching -- for example to identify homologs to a query sequence. The programs are not generally useful for motif- style searching.
      • BLAST at EDGP. This server supports both the "original" Blast programmes which do not allow gaps (NCBI), as well as the "newer" versions, namely Blast2 (WU). 
    • eCis-analyst is a tool for finding clustered transcription factor binding sites in the Drosophila melanogaster and Drosophila pseudoobscura genomes.
    • Ensembl Fruitfly site is a compendium of data from different sources: BDGP, FlyBase, DHGP, etc, integrated into the Ensembl system to allow people to access the Fly genome through the Ensembl user interface (both for visualisation and data mining) and to provide cross-species integration throught comparative genomics resources (such as homologous gene links and family pages).
    • Fly Enhancer is a search engine designed to find clusters of binding sites (or any sequences of nucleotides) in the Drosophila melanogaster genome. 
    • GrailEXP (Grail Experimental Gene Discovery Suite) is a software package that predicts exons, genes, promoters, polyAs, CpG islands, EST similarities, and repetitive elements within DNA sequence.
    • InterPro proteome comparisons for any of the complete proteomes, including Drosophila.
    • IUBio Biosequences section: Search and fetch DNA and protein sequences at/from major Databases:
      • FastA Search for sequence homology to predefined sections of biosequence databanks, using FastA software.
    • Proteomes & Genomes Fasta at EBI can be limited to Drosophila Proteome or Genome. 
    • STAG-Drosophila  "Search Texts in All over the GenomeNet" a metasearch interface from Japan, allowing to perform a simultaneous Drosophila-related text query of the following databases: GenBank, EMBL, EPD, RefSeq, SWISS-PROT, PIR, PRF, PDBSTR, PROSITE, PRINTS, COMPOUND, ENZYME, GENES, GENOMES, BRITE, OMIM, LITDB, PDB, TRANSFAC, PMD, AAindex, Pfam.
    • Two hybrid interaction map of the Drosophila Proteome. CuraGen Corporation.
  • Genome Annotation Databases:
    • Apollo Genome Annotation and Curation Tool. Apollo is a genome annotation viewer and editor. It was developed as a collaboration between the Berkeley Drosophila Genome Project (part of the FlyBase consortium) and The Sanger Institute in Cambridge, UK.  Apollo allows researchers to explore genomic annotations at many levels of detail, and to perform expert annotation curation, all in a graphical environment. It was used by the FlyBase biologists to construct the Release 3 annotations on the finished Drosophila melanogaster genome, and is also a primary vehicle for sharing these annotations with the community.
    • Drosophila Genomes Annotation & Sequences at FlyBase, former GadFly 
    • euGenes  Genomic Information for Eukaryotic Organisms. The goal of this developing site is to provide a common interface for the major model eukaryotic organism databases, which include Drosophila melanogaster (FlyBase), Homo sapiens (NCBI), Mus musculus (MGD), Arabidopsis thaliana (AtDB), Caenorhabditis elegans (ACeDB), Saccharomyces cerevisiae (SGD & YPD) and Danio rerio (ZFIN).
    • ERGO, Functional Overview of Drosophila melanogaster Genome. ERGO is a curated database of public + proprietary genomic DNA, with connected similarities, functions, pathways, functional models, clusters and more. The system presents these data interconnected with WWW hyperlinks but also allows searches and comparisons. Users may annotate and comment genes and pathways, but cannot currently edit sequences. It is being actively developed by Integrated Genomics Inc. (NB: an integrated version of WIT, a.k.a. IGwit; covers 80 genomes)
    • Full Euchromatic Expression Profile of Drosophila Melanogaster
    • GadFly  Genome Annotation Database of Drosophila, BDGP, with mirror at FlyBase NB: GadFly is being replaced by Gbrowse--a FlyBase Genome Browser. See also Apollo.
    • Gbrowse--a FlyBase Genome Browser.
    • GeneQuiz  of Drosophila melanogaster Genome
    • GO  Gene Ontology is a dynamic controlled vocabulary that can be applied to all eukaryotes. The three organizing principles of GO are molecular function, biological process and cellular component. Molecular function describes the tasks performed by individual gene products (e.g. transcription factor, DNA helicase). Biological process describes broad biological goals (such as mitosis or purine metabolism). Cellular component encompasses subcellular structures, locations, and macromolecular complexes (e.g. nucleus, telomere).
    • BDGP GO Browser provides query interface to the ontologies with a presentation of the gene products associated with GO terms by the collaborating databases
    • Infogene  Predicted and annotated Drosophila genes and proteins from Softberry Inc. 
    • KEGG-Genes A list of Drosophila genes according to the KEGG classification of metabolic and regulatory pathways
    • KEGG-DBGET Search  An advanced search of the Drosophila melanogaster KEGG Genes Database, Institute for Chemical Research, Kyoto University, Japan
    • Lifecycle database, which contains gene expression data for every stage of the Drosophila melanogaster life cycle
    • Proteome Analysis of Drosophila melanogaster @ EBI. The Proteome Analysis database has been set up to provide comprehensive statistical and comparative analyses of the predicted proteomes of fully sequenced organisms. The analysis is compiled using InterPro, CluSTr and GO, and is performed on the non-redundant complete proteome sets of SWISS-PROT and TrEMBL entries. 
    • TIGR DGI  The TIGR Drosophila Gene Index integrates research data from international Drosophila EST sequencing and gene research projects. The ultimate goal of the TIGR Gene Index projects, including DGI, is to represent a non-redundant view of all Drosophila genes and data on their expression patterns, cellular roles, functions, and evolutionary relationships.
  • Specialized Functional Annotation Databases:
    • BDGP in situ Database: Patterns of gene expression in Drosophila embryogenesis
    • DMPL Drosophila Membrane Protein Library is a collection of polytopic membrane protein sequences (containing two or more predicted membrane spanning domains) from Drosophila melanogaster. The protein sequences have been clustered into families based on sequence homology and the families have been assigned to functional categories where possible
    • DRSC Drosophila RNAi Screening Center.
    • FlyBrain  An Online Atlas and Database of the Drosophila Nervous System, with mirrors in Germany and Japan
    • FlyEx  Database of Segmentation Gene Expression in Drosophila.FlyEx stores quantitative data on gene expression in segmentation genetic network
    • FlySeq P Element Mapping Project
    • FlyView  is an image database on Drosophila development and genetics, especially on the expression patterns of genes (enhancer trap lines, cloned genes). All images are accompanied by text descriptions that can be used for searching. Currently FlyView  offers more than 3700 pictures from 796 enhancer-trap lines, including 235 lines from the BDGP and 400 lines from the GXP, which are available from the Bloomington stock center.
    • Homophila: Human Disease to Drosophila Genes Database.  The purpose of the Homophila database is to utilize the sequence information of human disease genes from the Online Mendelian Inheritance in Man (OMIM) database in order to determine if sequence homologs of these genes exist in the current Drosophila sequence database FlyBase.
    • DRES (broken link) Drosophila Related Expressed Sequences. Human cDNA clones homologous to Drosophila mutant genes
    • MitoDrome The MitoDrome database has been developed with the aim to annotate the complete set of Drosophila melanogaster nuclear genes encoding for mitochondrial proteins in order to contribute to their functional characterization.
    • Microarrays:
      • FlyChip  project is a publicly funded resource and its principal aim is to provide a non-profit microarray resource for the UK Drosophila research community. The aim is to accumulate a database of Drosophila  microarray expression results which will be available for data mining.
      • Drosophila Microarray Project. A major goal of this project is to define the gene expression patterns of every gene in the genome that can be detected in whole animals using DNA microarrays. The complete Drosophila life cycle will be analyzed.

 
 
 
 
Nomenclature and Taxonomy:
 
  • Nomenclature:
    • Genetic Nomenclature  The rules for the genetic nomenclature of Drosophila melanogaster, as adopted by FlyBase. The rules are based on those published in Lindsley and Zimm (1992), The genome of Drosophila melanogaster
    • Anatomical Nomenclature, as well as terms used in defining Developmental Stages, Germ Layers, Organ Systems, Segment and Adult Morphology, etc. FlyBase.
    • Drosophila anatomomy embryo stages (PDF file). A list of terms for cell and tissue types, by J. Bard &V. French, adapted form Campos-Ortega & Hartenstein 1985
    • GO  Gene Ontology is a dynamic controlled vocabulary that can be applied to all eukaryotes. The three organizing principles of GO are molecular function, biological process and cellular component. Molecular function describes the tasks performed by individual gene products (e.g. transcription factor, DNA helicase). Biological process describes broad biological goals (such as mitosis or purine metabolism). Cellular component encompasses subcellular structures, locations, and macromolecular complexes (e.g. nucleus, telomere).
      • BDGP GO Browser provides query interface to the ontologies with a presentation of the gene products associated with GO terms by the collaborating databases
  • Taxonomy:
    • Taxonomy of Drosophila melanogaster group
    • Taxonomyof Drosophilidae, preferred common name: pomace flies

 
 
 
 
Maps, Atlases, and Pictures:
  • Maps:
  • Atlases:
    • FlyBrain  An Online Atlas and Database of the Drosophila Nervous System, with mirrors in Germany and Japan
    • FlyMove  This site is dedicated to the visual presentation of embryonic development of Drosophila melanogaster. Intended for biology students from the 3rd year onwards. Quicktime movies and short explanatory texts help to see and understand development
  • Pictures:
    • Fly Morph-O-Genesis, a series of S.E.M. images of Drosophila embryos in the form of "movies" of wild type and mutant fly embryogenesis. These sequences show how fly embryogenesis proceeds
    • Mutant Fruit Flies Exploratorium Exhibit. Drawings of the mutants used in introductory courses.
    • BDGP in situ Database: Patterns of gene expression in Drosophila embryogenesis

      •  

 
 
 
 
Stocks,  Mutants, and Reagents (see also sections: Protocols and Reagents)
 
  • Stock Centers:
    • Bloomington The Bloomington Drosophila Stock Center at Indiana University, a major repository of Drosophila melanogaster stocks in the US. 
    • Szeged Drosophila Stock Centre
      • Szeged  P-element Stocks: recessive lethal P-element induced mutants (on chromosomes 2 and 3) generated in Istvan Kiss' and in Peter Maroy's laboratories. The Centre also carries the collection of Pernille Rorth's EP element insertion lines.
    • DrosDel Drosophila Isogenic Deficiency Kit. DrosDel deletion kit is being constructed using RS (re-arrangement screen) P-elements originally described by Golic and Golic (1996).
    • Tucson Center -- species. 1293 stocks are listed of which 1261 are available.
    • Umeå  The European Drosophila Stock Centre at Umea carries the following categories of Drosophila melanogaster stocks: "general stocks", maternal-effect lethals, zygotic lethals, wild-type, as well as non-melanogaster species
      • Umeå --> Bloomington Stock Number Conversion Table. The list includes the Umeå stock numbers for most of the Umeå stocks that will be transferred to Bloomington. If the stock has completed quarantine and is available for shipping the Bloomington stock number is provided. To order, use the Bloomington stock number, not the old Umeå number. 
    • DGR, J*Fly  "Drosophila Genetic Resources" from Japan National Institute of Genetics maintains Stock Lists of Wild type Drosophila stocks and Drosophila melanogaster mutant stocks available in Japan from NIG and individual labs.
    • Kyoto: Drosophila Genetic Resource Center
    • EDSC Ehime DrosophilaSpecies Center of Japan
  • Mutant Collections:
    • Tübingen  Drosophila stock collection
    • Exelixis collection is now at Harvard Medical School. The EP lines allow GAL4-mediated overexpression of genes adjacent to the EP transposon and were generated by Pernille Rorth while at the Carnegie Institution of Washington. These stocks also can be obtained from the Szeged P-element Insertion Stock Centre
    • FlySeq P Element Mapping Project
    • FlyView is the beginning of an image database on Drosophila development and genetics, especially on expression patterns of genes (enhancer trap lines, cloned genes).The concept of FlyView includes compatibility to FlyBase, the main Drosophila database. 
    • GFP Flytrap web site acts as a central data repository for Drosophila melanogaster transgenic lines being created using an intron protein trap strategy. 
    • Genexel -- Commercial Drosophila mutant collection. GenExel's fly stock library comprises nearly 25,000 mutant lines selected from 100,000 independent EP stocks, providing extensive genome coverage. Price: $2,000 per mutant line, less if number of stocks >10.
    • Gene Disruption Project / P-element Screen Database of the Bellen/Rubin/Spradling labs.
  • DNA clones and Libraries: see also section  Reagents > Clones and Libraries
    • DGRC --The Drosophila Genomics Resource Center will serve the Drosophila research community by: (a) collecting and distributing DNA vectors, cDNAs, and ESTs; (b) collecting and distributing cell lines; (c) manufacturing and distributing microarrays; (d) assisting scientists in the use of these materials; and (e) sponsoring and testing emerging genomics technologies on behalf of the community.
    • BDGP Resources: BAC, YAC, P1, cosmid, cDNA clones and filters.
    • genomic BAC  The DNA was prepared from embryos. The insert sizes range from 75 - 150 kb, and the library consists of approx. 23,400 clones, providing an approximate 10-fold genome coverage. The library is available  as two high density double spotted gridded filters for screening by hybridisation.
    • genomic cosmids  Drosophila cosmid genomic clones and filters: This library has an estimated average insert size of 35kb and contains approximately 18,000 clones providing a 4-fold coverage of the genome.
    • testes  cDNA  This library was prepared from dissected testes from 1-5 day old flies. Approximately 3930 clones are available from plates and on one double-spotted high density filter for screening by hybridisation. 
  • Cell Lines:
  • Antibodies: see also section  Reagents > Antibodies
    • Developmental Studies Hybridoma Bank at The University of Iowa, carries many Drosophila antibodies
    • Hybridoma Data Bank and ATCC, provide a comprehensive directory of information on hybridomas and other cloned cell lines and their immunoreactive products, such as Mabs, including Drosophila
    • BD Biosciences/Pharmingen mAbs: Antibodies for Drosophila Research.
    • segmentation antibodies  A collection of antibodies against segmentation gene products made by D. Kosman, S. Small, and J. Reinitz. WWW information  from the East Asian Distribution Center

 
 
 
 
Methods and Protocols(see also sections: Protocols and Reagents)
  • Carthew Lab Manual
  • Carroll Lab Methods
  • Protocols from the Drosophila Virtual Library
  • M-FISH Multiplex Fluorescent In Situ Hybridization Protocol for Drosophila Embryos
  • media recipes  from the Bloomington Drosophila Stock Center
  • cloning vectors  plasmid and cosmid cloning vectors for P or H transformation from FlyBase. Including derivatives of Carnegie, CaSpeR, Hsp, neo, lacZ, FLP/FRT, GAL4/UAS, cell ablation, cell culture, enhancer traps, transposase sources, etc.
  • Vector DB contains annotations and sequence information for many vectors commonly used in molecular biology. Information for more than 2600 vectors is available with search facilities. Vectors which are also in GenBank have direct links to that database via NCBI's Entrez browser.

 
 
 
 
Meetings and Societies 
 

 
 
 
 
Labs,  People, and Institutions
  • Drosophila Workers A Flybase section, provides address and e-mail contacts for Drosophila researchers. 
  • Drosophila Labs  Links to the Drosophila Research Labs on the Web from the Drosophila Virtual Library
  • Japan Japanese Drosophila labs with lists of fly stocks they maintain

    •  
Newsgroups:
  • dros/bionet  Drosophila Newsgroup searchable Archive, with current postings at the very bottom of the page. Alternative search is available from the FlyBase. An alternative view/search is also available at Google.
  • cellbiol/bionet  Cell Biology searchable Archive, with current postings at the very bottom of the page
  • cytonet/bionet  The cytoskeleton, plasma membrane and cell wall
  • fluorpro/bionet  Fluorescent proteins & bioluminescence
  • methods/bionet  Requests for information on methods and lab reagents.

 
 
 
 
Literature (see also section: Journals)
  • Red Book  Full text of the so-called "Red Book": Dan Lindsley and Georgianna Zimm (1992) The Genome of Drosophila melanogaster.
  • DIN  Drosophila Information Newsletter
  • DIS  Drosophila Information Service - full text of Vol.84, partial of Vols 82-83, more forthcoming.
  • DIS-indexes  Cumulative Subject Index and Drosophilid Species Index for Volumes 1 to 71(1992). Key words were drawn from article titles.
  • Genesis (Special Issue: GAL4/UAS in Drosophila.) Volume 34, Issue 1-2, 2002.

 
 
 
 
Introductory and Educational Resources

 
 
 
 
Portal Websites
  • Drosophila Virtual Library,  a comprehensive portal to the Drosophila-related information on the Web
  • Jfly is a data depository for Drosophila researchers. The emphasis is placed on collecting information and documents for Japanese-speaking fly community.

 
 
 
 
Misc.
     

 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 

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