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FlyBase

FlyBase is an online

  • Flybase A Database of Drosophila Genes & Genomes

External links

See also

  1. ^ Crosby, Madeline A., and Rachel A. Drysdale. "FlyBase: Genomes by the Dozen." Oxford Journals. Oxford University Press. Web. 27 Sept. 2011. .
  2. ^ Wilson, Robert J., Joshua L. Goodman, and Victor B. Strelets. "FlyBase: Integration and Improvements to Query Tools." Pubmed.gov. NCBI, Jan. 2008. Web. 27 Sept. 2011. .
  3. ^ Drysdale, R., and FlyBase Consortium. "FlyBase : a Database for the Drosophila Research Community." Pubmed.gov. National Center for Biotachnology Information. Web. 27 Sept. 2011. .
  4. ^ Drosophila, Using. "An Introduction to Drosophila Melanogaster." BIOLOGY.ARIZONA.EDU. Web. 23 Nov. 2011. .
  5. ^ The FlyBase Consortium. "FlyBase: A Drosophila Database." Oxford University Press, 1997. Web. .
  6. ^ Drysdale, Rachel; Flybase Consortium (2008-07-19). Dahmann, Christian, ed. "FlyBase : a database for the Drosophila research community.". Methods in Molecular Biology (Totowa, New Jersey, USA: Humana Press) 420: 45–59.  
  7. ^ [1]
  8. ^ [2]
  9. ^ "FlyBase: Site Map and Resource Guide." FlyBase Homepage. Web. 23 Nov. 2011. .
  10. ^ Hunter, W. B. "Aphid Biology: Expressed Genes from Alate Toxoptera Citricida, the Brown Citrus Aphid." Insectscience.org. Web. 23 Nov. 2011. .
  11. ^ The Gene Ontology. Web. 23 Nov. 2011. .
  12. ^ Tweedie, Susan. "FlyBase: Enhancing Drosophila Gene Ontology Annotations." Oxford Journals | Life Sciences | Nucleic Acids Research. Web. 23 Nov. 2011. .

Notes and references

The following is only two of many examples of research that is related to or uses FlyBase: 1. The first is a study of expressed genes from alate Toxoptera citricida, more commonly known as the brown citrus aphid. The brown citrus aphid, is considered the primary vector of citrus tristeza virus, a severe pathogen which causes losses to citrus industries worldwide. The winged form of this aphid can fly long distances with the wind, enabling them to spread the citrus tristeza virus in citrus growing regions. To better understand the biology of the brown citrus aphid and the emergence of genes expressed during wing development, researchers undertook a large-scale 5′ end sequencing project of cDNA clones from winged aphids. Similar large-scale expressed sequence tag (EST) sequencing projects from other insects have provided a vehicle for answering biological questions relating to development and physiology. Although there is a growing database in GenBank of ESTs from insects, most are from Drosophila melanogaster, with relatively few specifically derived from aphids.The researchers were able to provide a large data set of ESTs from the alate (winged) brown citrus aphid and have begun to analyze this valuable resource. They were able to do this with the help of information on Drosophila melanogaster in FlyBase. Putative sequence identity was determined using BLAST searches. Sequence matches with E-value scores ≤ −10 were considered significant and were categorized according to the Gene Ontology (GO) classification system based on annotation of the 5 ‘best hit’ matches in BLASTX searches. All D. melanogaster matches were cataloged using FlyBase. Nearly all of these ‘best hit’ matches were characterized with respect to the functionally annotated genes in D. melanogaster using FlyBase. Genetic information is crucial to advancing the understanding of aphid biology, and will play a major role in the development of future non-chemical, gene-based control strategies against these insect pests.[10] 2.Enhancing Drosophila Gene Ontology Annotation: What gene products do and where they do it are important questions for biologists. The Gene Ontology project was established 13 years ago in order to summarize this data consistently across different databases by using a common set of defined vocabulary terms. They also encode relationships between terms. The Gene Ontology Project is a major bioinformatics initiative with the aim of standardizing the representation of gene and gene product attributes across species and databases. The project also provides gene product annotation data from GO consortium members.[11] />.) This is where FlyBase comes in. FlyBase was one of the three founding members of the Gene Ontology Consortium. GO annotation comprises at least three components: a GO term that describes molecular function, biological role or subcellular location; an ‘evidence code’ that describes the type of analysis used to support the GO term; and an attribution to a specific reference. GO annotation is useful for both small-scale and large-scale analyses. It can provide a first indication of the nature of a gene product and, in conjunction with evidence codes, point directly to papers with pertinent experimental data. The current priorities for annotation are: homologs of human disease genes, genes that are highly conserved across species, genes involved in biochemical/signaling pathways, and topical genes shown to be of significant interest in recent publications. FlyBase has been contributing GO annotations to the project since it started in August 2006. GO annotations appear on the Gene Report page in FlyBase. GO data are searchable in FlyBase using both TermLink and QueryBuilder. The GO is dynamic and can change on a daily basis, for example the addition of new terms. To keep up, FlyBase loads a new version of the GO every one or two releases of FlyBase. The GO annotation set is submitted to the GOC at the same time as a new version of FlyBase is released.[12]

Related Research

FlyBase has a very useful Site Map to help navigate through the content of the website.[9]

There are two main query tools in FlyBase. The first main query tool is called Jump to Gene (J2G). This is found in the top right of the blue navigation bar on every page of FlyBase. This tool is useful when you know exactly what you are looking for and want to go to the report page with that data. The second main query tool is called QuickSearch. This is located on the FlyBase homepage. This tool is most useful when you want to look up something quickly that you may only know a little about. Searching can be performed within D. melanogaster only or within all species. Data other than genes can be searched using the ‘data class’ menu.

When looking for cytology there are two main tools available. Use Cytosearch when looking for cytologically-mapped genes or deficiencies, that haven’t been molecularly mapped to the sequence. Use Gbrowse when looking for molecularly mapped sequences, insertions, or Affymetrix probes.

Search Strategies - Gene reports for genes from all twelve sequenced Drosophila genomes are available in FlyBase. There are four main ways this data can be browsed: Precomputed Files, BLAST, Gbrowse, and Gene Report Pages. Gbrowse and precomputed files are for genome wide analysis, bioinformatics, and comparative genomics. BLAST and gene report pages are for a specific gene, protein, or region across the species.

FlyBase contains a complete annotation of the Drosophila melanogaster genome that is updated several times per year.[6] It also includes a searchable bibliography of research on Drosophila genetics in the last century. Information on current researchers, and a partial pedigree of relationships between current researchers, is searchable, based on registration of the participating scientist.[7] The site also provides a large database of images illustrating the full genome, and several movies detailing embryogenesis.[8]

Contents

Drosophila melanogaster has been an experimental organism since the early 1900s, and has since been placed at the forefront of many areas of research.[4] As this field of research spread and became global, researchers working on the same problems needed a way to communicate and monitor progress in the field. This niche was initially filled community newsletters such as the Drosophila Information Service (DIS), which dates back to 1934 when the field was starting to spread from Drosophila melanogaster. FlyBase also receives support from the Medical Research Council, London.[5] In 1998, the FlyBase consortium integrated the information into a single Drosophila genomics server.

Background

Contents

  • Background 1
  • Contents 2
  • Related Research 3
  • Notes and references 4
  • See also 5
  • External links 6

FlyBase is one of the organizations contributing to the Generic Model Organism Database (GMOD).

in the United Kingdom. University of Cambridge in the United States, and Indiana University and Harvard University researchers and computer scientists at Drosophila The FlyBase project is carried out by a consortium of [3]

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