SITE MAP AND RESOURCE GUIDE FOR FLYBASE
Updated 1 October 2004
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RESOURCE CATEGORIES. Each entry is linked to the listed resource. For a brief description of each resource, see map at right or go directly to the descriptions. FLYBASE SEARCHES MAJOR SECTIONS OF FLYBASE SEQUENCES ANALYSIS & ANNOTATION IMAGES FLYBASE REPORTS BY MAP POSITION STOCK CENTERS AND COLLECTIONS DROSOPHILA GENOME PROJECTS TERMS AND NOMENCLATURE FLYBASE HELP, DOCUMENTS & DOCUMENTATION SITES FOR SCIENTISTS NEW TO DROSOPHILA LISTS FOR BROWSING |
Alphabetical index of FlyBase and related resources. Descriptions and links to non-FlyBase resources have a light blue background. Each entry is linked to a brief description of the resource, which includes a link to that resource. For direct links to FlyBase resources, see the list at left. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Alphabetical listing of FlyBase and related resources, with descriptions of the resources and links to those resources. Aberrations. Search for chromosomal deficiencies, duplications, inversions, translocations or transpositions. Also, search for balancer chromosomes. Aberrations displayed on a cytological map. View aberrations (deficiencies, duplications, inversions, translocations and transpositions) arranged on a cytological map. Each band is hyper linked to a listing of the Aberrations in that region, with further links to individual reports. Aberrations listed by cytological location. Browse a list of deletions,duplications, and rearrangements organized by map position. Each entry is linked to an aberration report, with links to stock reports, when available. Aberrations search (all options). Search for Aberrations by ID number, symbol, name, phenotype, allele, reference, species, cytological location or aberration class. Or, browse a list of all aberration reports. Alleles search. Use this form to search for alleles by ID number, symbol, name, phenotype reference, allele class, mutagen, or phenotype class. Allied data and related databanks. A listing of data and databases that have been contributed by members of the research community that are not explicitly part of FlyBase, but which might prove useful to other members of the community. Anatomy images browser. View images organized by developmental stage or organ system. Image reports include annotated image and a listing of associated vocabulary terms. Anatomy terms hierarchy. Browse the anatomical term hierarchy from the top level or the following subsets: developmental stage, germ layer, organ system, tagma or adult external morphology. Vocabulary reports for each term include the genes, alleles, reporter constructs, transcripts, proteins and available stocks associated with that vocabulary term. Anatomy terms with images. View images from all life stages together with a list of anatomy terms associated with the image. Annotated genome. Use the Apollo genome annotation and curation tool to explore genomic annotations in a graphical environment or use GBrowse to view graphical displays of sequence-mapped features in specified regions of the genome. Use annotation query form for additional search options. Announcements and news. This site contains a listing of announcements by FlyBase (including available jobs), upcoming meetings, and Drosophila Board business. Apollo genome annotation tool A Java application for geneome annotation viewing and editing from the BDGP. Balancer stocks (Bloomington). Browse a list of Bloomington Stock Center stocks containing balancer chromosomes. Balancers search. Search for balancer chromosomes. Resulting balancer reports list available stocks. Basic search. Use this search form if you don't know exactly which section of FlyBase to search. A search such as this may generate a large number of hits, and may require further refinement. Help is available. Batch/bulk download. Use a form to batch download FlyBase reports by FlyBase ID, Drosophila Gene Collection (DGC) or Computed Gene (CG) symbol. Or, batch download sequences by FlyBase ID, DGD or CG symbol. Reference Manual D contains help with batch downloading of reports. BDGP. The home page of the Berkeley Drosophila Genome Project. The BDGP is a consortium of the Drosophila Genome Center. BLAST Search BLAST search for Drosophila sequences. Browse FlyBase reports. Browse complete listing of FlyBase reports organized by report class. View all aberration reports, annotation reports, gene reports, insertion reports, polypeptide reports, reference reports or transcript reports. Also browse reports of new genes, recently updated gene reports, and recently updated aberration reports. Citing FlyBase. Suggested reference for FlyBase in publications. Cytological maps. View a graphical display of genes, deficiencies, duplications, inversions, translocations and transpositions, and other aberrations placed on the chromosomal arms. Each mapped object is linked to a data report. CytoSearch. Search the database for genes, alleles, clones, deficiencies, duplications, inversions, translocations and transpositions by map position. A search results in a listing of reports, together with available stocks. Deficiency kit stocks (Bloomington). A listing of all stocks used in the deficiency kits available from the Bloomington Stock Center. Drosophila Gene Collection (BDGP). Obtain information about the collection of non-redundant cDNA clones. Search for specific sequences and find a nearby source of the clones. Drosophila life cycle. View a diagram of the life cycle of Drosophila melanogaster, with links to developmental stage vocabulary reports. Drosophila network news search form. Search for bionet articles archived on FlyBase by text, author, subject, or year submitted. Drosophila Genomics Resource Center The Drosophila Genomics Resouces Center collects and discributes DNA clones and cell lines and manufactures and distributes microarrays for use by the Drosophila community. The DGRC is not a part of FlyBase or the Bloomington Drosophila Stock Center. Drosophila resources. A list of links to Drosophila network resources, which include comparative analysis and genome databases, sequence analysis, and images. Also included are links to material resources such as DNA clones, filters and libraries as well as Drosophila stocks. Drosophilid species abbreviations. A listing of Drosophilid species and the abbreviations used by FlyBase. Use these abbreviations to search for genes or aberrations in other fly species. Drosophilidae species drawings. Folder containing images of Drosophilidae from the southwestern United States and northern Mexico. Embryogenesis electron micrographs. Folder with a collection of labeled and unlabeled electron micrographs depicting gastrulation (dorsal or lateral), head involution, mesoderm invagination, and bcd- and ftz-embryogenesis. Embryogenesis line drawings. Folder containing 9 line drawings used to create the embryogenesis animated movie. Embryogenesis movies by Ji, Hurley, Schubiger, Squirrell and White (500 MB) or Embryogenesis movies folder with movies by Giacoletti and Macri. This folder contains .mpg files depicting embryogenesis , gastrulation-dorsal , gastrulation-lateral , gastrulation-ventral , head involution , ftz-gastrulation and bcd-gastrulation. EST project cDNA Expression patterns (BDGP). Search for CK cDNAs (a library of rough ER-bound messages) expressed in selected tissues or organs. Results include sequences and in situ images when available. To find genes, alleles, reporter constructs, transcripts, proteins or stocks associated with a vocabulary term, use the gene expression pattern search. EST project cDNAs (BDGP). Search for cDNAs by clone ID number, dbEST accession number, GenBank accession number or keyword. Existence-uncertain genes. Browse a list of genes with data too limited to verify their existence. FlyBase publications. A listing of the commercially published documents concerning FlyBase and FlyBase Consortium projects. FlyBase Reference Manual. FlyBase Reference Manual contains the documentation of FlyBase, including a description of the database and the classes of data that may be searched or browsed as well as help in successfully searching the database. FlyBase structure and data. Reference Manual B, a detailed description of the structure of the FlyBase databases. Function, component, process, & structure in Drosophila. (Gene Ontology) Search for genes by the gene product's molecular function, cellular component, biological process (Gene Ontology) or structure. Also browse a list of genes organized by molecular function, cellular component, biological process or structure. GBrowse GBrowse is a genome browser that provides graphical displays of sequence-mapped features in specified regions of the genome. Gene expression patterns. Find genes, alleles, reporter constructs, transcripts, proteins and stocks associated with a vocabulary term. The results list can be further defined by developmental stage or specific body part. Gene Products. Search for polypeptides or transcripts by symbol, ID number, gene, allele, body part, or reference. Browse a list of all polypeptides or transcripts. Genes. Search for all Drosophila genes, alleles, transcripts and polypeptides. Included are searches for genes based on expression patterns or cellular localization and molecular function. Genes by symbol. Browse a list of all FlyBase genes listed by gene symbol. This list is case-sensitive. Genes displayed on a graphical map. View a display of genes placed on the chromosomal arms. Each map position is linked to the gene reports for the genes in that region. Genes listed by cytological location. Browse a list of genes organized by cytological location. Each gene name is linked to a gene report, and links to available stocks are listed as well. Genes search (all options). Use this query form to search for genes by symbol, name, function, phenotype, reference, or ID number. The search may be extended to include map position, affected body part, gene ontology (GO) terms, and/or gene class. Or, browse a list of all FlyBase gene reports. Genetic nomenclature for Drosophila. A description of the standards for genetic nomenclature in Drosophila used by FlyBase. Genome annotation and sequences Search for annotation reports by ID, symbol, cytological location, function, transcript size or peptide size. Also, browse annotation reports or view annotations graphically. Genome annotation search (all options). Search the database for individual annotations or features, or for groups of genes and features with particular cytological locations, molecular functions, protein domains or peptide sizes. Or, batch download annotation reports by FlyBase ID. Getting started with FlyBase. Reference Manual A contains information about FlyBase, how to use it and how to contact FlyBase. Glossary of anatomical terms. A glossary of anatomical terms containing some of the controlled vocabulary used by FlyBase, with links to FlyBase term reports for anatomy and development terms. Help and documents. A listing of help documents available for FlyBase users. Historical files. FlyBase contains a number of files of historical interest, including "Fruit flies in your Java", old map data and FlyBase working papers. Insertion search. Search for insertions by symbol, comment, ID number, gene, allele, aberration, transposon/transgene construct, transcript, progenitor or references. Browse insertions listed by map position, or a list of all insertion reports. Interactive Fly (T.B. Brody). A guide to the genes involved in Drosophila development . Genes are listed alphabetically, grouped according to biochemical function, or by developmental pathways. Also included are detailed descriptions of developmental stages and processes. Introduction to Drosophila research. A list of hyperlinks to documents that contain basic information about Drosophila and its usefulness to the scientific community. Journal/book abbreviations. Search for the full titles of references using abbreviations, or find the abbreviation for a reference. Mapping stocks (Bloomington). A listing of Bloomington stocks that are useful for a variety of mapping purposes, with links to stock reports. Maps. A listing of the tools used to find Drosophila genetic elements based on their locations on the chromosomal arms. Mirrors of FlyBase. Select alternative FlyBase servers closer to you for quicker access. Molecular maps by cytological location. Browse a list of molecular maps organized by cytological location. Each entry is linked to a molecular map showing gene structure information, aberration breakpoints, insertions, regulatory elements and/or rescue fragments curated from the literature. Mutant embryogenesis micrographs. Folder containing electron micrographs of embryogenesis in bcd and ftz mutants. Mutant head images. Folder containing images of antp, antp-pb and wild-type adult heads. Naturally occurring transposons. Browse a list of transposons occurring naturally in Drosophila melanogaster or related fly species. People. Search for Drosophila workers by name, institution, state or country, add information for a new Drosophila worker or update your address and information. Polypeptides search. Search for polypeptide reports by symbol, ID number, gene, allele, transcript, progenitor, reference, body part where expressed or subcellular location. Or, browse a list of all polypeptide reports. Portable FlyBase server. FlyBase-NG can be copied, run on your local computer or informatics center, and is designed for automatic updates to keep it current. It works on popular Unix systems including MacOSX, Linux and Solaris. Reference Manual E has directions for setting up your own copy of FlyBase-NG.. References search. Search research literature, including journals, books, abstracts and personal communications, by author, title, journal, publication type or year published. Also search for journal/book abbreviations. Or, browse a list of all reference reports. Search FlyBase. All FlyBase searches may be accessed from this site. Sequence features from the literature. Genes are listed in alphabetical order by symbol, together with a thumbnail image of the annotation of the gene. Selecting a gene or image will generate a larger map; full reports, including sequences, are found by clicking on the map entities. Or, view the gene list without the thumbnail images.. Stock Center-Bloomington home page or order form. Stock Center-Kyoto Home page of the Drosophila Genetic Resource Center in Kyoto. Stock Center-Szeged Home Page or stock order form. The Szeged stock center distributes P insertion strains. Stock Center-Tucson. Search and order stocks of approximately 270 non-melanogaster Drosophilid species. Stocks Search for Drosophila stocks available from a number of sources. Help with searches is available. Also, browse stock center folders or individual lab stocks folders. Stocks from individual laboratories. This folder contains stock lists from individual laboratories. These stocks may be obtained directly from the individual labs, using the information found in documentation and contact information for laboratory stock lists. Stocks search (all options). Search for Drosophila stocks by stock number, symbol, date added to the collection, or cytological location. Included are stock lists from Bloomington Drosophila Stock Center, Szeged Drosophila Stock Center and various laboratories. Help with searches is available. Stocks-Special Collections. Browse special stock collections from the Baylor/BDGP Gene Disruption project, the DrosDel project (isogenic deficiency lines), the FlyTrap GFP protein trap lines, or the FlyView enhancer trap lines. Suggestions for authors. This help document contains suggestions for describing and naming genes, alleles and constructs in publications. Transcripts search. Search for transcript reports by symbol, ID number, gene, allele, insertion, polypeptide, reference, or body part where expressed. Or browse the entire list of transcript reports. Transformation constructs from DIS 78, 1997. Browse a list constructs published in DIS 78 with hyperlinks to current construct reports, annotated maps and sequence data, if available. Transgene construct search. Search for transgenes by ID number, symbol, name, gene, allele, insertion, progenitor, descendant or reference. Specific types of constructs (reporter, etc.) may also be searched. Transgenes and Transposons. Search for transgenes or insertions. Includes a listing of naturally occurring transposons from Drosophila melanogaster as well as related species. Transposon insertions listed by cytological location. Browse a list of transposon insertions organized by map position, with links to insertion and stock reports. Using FlyBase on the Web. Reference Manual C describes FlyBase search tools and the types of reports available. Wild stocks (Bloomington). A listing of the wild type stocks available from the Bloomington Drosophila Stock Center, with links to individual stock reports. Wild-stocks data. This file contains data on wild-type stocks and chromosomes of D. melanogaster, and inbred mutant strains used for genetic studies.
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