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FlyBase: anatomical data, images and queries
Department of Biology, Indiana University 1001 E 3rd Street, Bloomington, IN 47405-7005, USA
*To whom correspondence should be addressed. Tel: +1 812 856 2381; Fax: +1 812 855 6705; Email: ggrumbli{at}bio.indiana.edu
Received September 15, 2005. Revised October 8, 2005. Accepted October 8, 2005.
FlyBase (http://flybase.org/) is a database of genetic and genomic data on the model organism Drosophila melanogaster and the entire insect family Drosophilidae. The FlyBase Consortium curates, annotates, integrates and maintains a wide variety of data within this domain. Access to the data is provided through graphical and textual user interfaces tailored to particular types of data. FlyBase data types include maps at the cytological, genetic and sequence levels, genes and alleles including their products, functions, expression patterns, mutant phenotypes and genetic interactions as well as aberrant chromosomes, annotated genomes, genetic stock collections, transposons, transgene constructs and insertions, anatomy and images, bibliographic data, and community contact information.
FlyBase-Harvard: W. Gelbart, M. Crosby, B. Matthews, S. Russo, D. Emmert, F. Smutniak, L. S. Gramates, K. Campbell, P. Zhou, R. Kulathinal, A. Schroeder, M. Zytkovicz, P. Zhang, L. Bitsoi, H. Zhang, S. St Pierre and A. Dirkmaat (Biological Laboratories, Harvard University, Cambridge, MA, USA). FlyBase-Cambridge: M. Ashburner, R. Drysdale, A. de Grey, G. Millburn, C. Yamada, D. Sutherland, R. Seal, R. Collins, P. Leyland and P. McQuilton (Department of Genetics, University of Cambridge, Cambridge, UK). FlyBase-Indiana: T. Kaufman, K. Matthews, V. Strelets, G. Grumbling, A. DeAngelo and J. Goodman (Department of Biology, Indiana University, Bloomington, IN, USA). FlyBase-Berkeley: G. Rubin, S. Lewis, N. Harris, S. Misra, C. Mungall, S. Shu and C. Smith (University of California at Berkeley, Berkeley, CA, USA).
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|
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|
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|
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|
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|
|
|
|
|
|
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|
|
|
|
|
|
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|
|
|
|
|
|
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|
|
|
|
|
|
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|
|
|
|
|
|
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|
|
|
|
 |
|
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|
|
|
|
|
|
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|
|
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|
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|
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|
|
|
|
|
|
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|
|
|
|
|
|
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|
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|
|
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|
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