Abstract

This proposal requests funding to expand the effort dedicated to sequencing the Drosophila genome. The ambitious scale-up is part of our plan to complete the sequence of the 120 megabases of the euchromatic genome of this central model organism shortly after the turn of the century. It is expected that the increase in sequencing production will come from both the additional number of people working on the project and from a steadily increasing sequencing efficiency. The increased efficiency will be achieved largely through the interdisciplinary interaction of the biology, automation, and computation groups at LBL. This section of the proposal describes the directed strategy that is being used, the current status of the automation and computation efforts, the manner in which the workforce is organized, and the costs associated with the production effort.

  Funding Agency

Agency
National Institute of Health (NIH)
Institute
National Human Genome Research Institute (NHGRI)
Type
Specialized Center (P50)
Project #
5P50HG000750-09
Application #
6410504
Study Section
Project Start
2000-12-03
Project End
2001-11-30
Budget Start
1998-10-01
Budget End
1999-09-30
Support Year
9
Fiscal Year
2001
Total Cost
$1,481,238
Indirect Cost

  Institution

Name
University of California Berkeley
Department
Type
DUNS #
094878337
City
Berkeley
State
CA
Country
United States
Zip Code
94704

  Publications

Hoskins, Roger A; Carlson, Joseph W; Wan, Kenneth H et al. (2015) The Release 6 reference sequence of the Drosophila melanogaster genome. Genome Res 25:445-58
Hoskins, Roger A; Carlson, Joseph W; Kennedy, Cameron et al. (2007) Sequence finishing and mapping of Drosophila melanogaster heterochromatin. Science 316:1625-8
Tomancak, Pavel; Berman, Benjamin P; Beaton, Amy et al. (2007) Global analysis of patterns of gene expression during Drosophila embryogenesis. Genome Biol 8:R145
Osoegawa, Kazutoyo; Vessere, Gery M; Li Shu, Chung et al. (2007) BAC clones generated from sheared DNA. Genomics 89:291-9
Yandell, Mark; Mungall, Chris J; Smith, Chris et al. (2006) Large-scale trends in the evolution of gene structures within 11 animal genomes. PLoS Comput Biol 2:e15
George, Janet A; DeBaryshe, P Gregory; Traverse, Karen L et al. (2006) Genomic organization of the Drosophila telomere retrotransposable elements. Genome Res 16:1231-40
Bergman, Casey M; Carlson, Joseph W; Celniker, Susan E (2005) Drosophila DNase I footprint database: a systematic genome annotation of transcription factor binding sites in the fruitfly, Drosophila melanogaster. Bioinformatics 21:1747-9
Pollard, Daniel A; Bergman, Casey M; Stoye, Jens et al. (2004) Benchmarking tools for the alignment of functional noncoding DNA. BMC Bioinformatics 5:6
Berman, Benjamin P; Pfeiffer, Barret D; Laverty, Todd R et al. (2004) Computational identification of developmental enhancers: conservation and function of transcription factor binding-site clusters in Drosophila melanogaster and Drosophila pseudoobscura. Genome Biol 5:R61
Harbison, Susan T; Yamamoto, Akihiko H; Fanara, Juan J et al. (2004) Quantitative trait loci affecting starvation resistance in Drosophila melanogaster. Genetics 166:1807-23

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