The overall goal of the integrated genome analysis project is to annotate the genomic sequence with features of biological interest in a cost- effective manner. We envision the use of a variety of gene-finding, sequence-feature-identification, and gene-disruption approaches in the process of striving towards an """"""""ultimate genome map"""""""" of Drosophila. This work has four components: (1) the use of insertional mutagenesis, primarily utilizing P-element enhancer trap constructs that also provide a window on the patterns of expression of the mutated genes, to conduct a gene disruption experiment of unprecedented scale in a metazoan organism; (2) the study of expressed sequence through the characterization of the sequence and expression pattern of cDNA molecules: (3) the development and testing of computational approaches to the algorithmic identification of expressed sequences, control regions, and other features of the DNA sequence; and (4) the development of informatics tools both to support the experimental process and to allow the presentation of up-to-date information on the annotated Drosophila genomic sequence to the world-wide user research community. This latter goal involves a collaboration with the FlyBase database group (W. Gelbart, PI) to develop a common product called the 'Encyclopaedia of Drosophila' as well as the assembly or development of tools to periodically re-analyze the completed Drosophila sequence in light of new information generated by our project or other researchers.

Agency
National Institute of Health (NIH)
Institute
National Human Genome Research Institute (NHGRI)
Type
Specialized Center (P50)
Project #
2P50HG000750-06
Application #
6272461
Study Section
Project Start
1997-12-01
Project End
1998-11-30
Budget Start
1997-10-01
Budget End
1998-09-30
Support Year
6
Fiscal Year
1998
Total Cost
Indirect Cost
Name
University of California Berkeley
Department
Type
DUNS #
094878337
City
Berkeley
State
CA
Country
United States
Zip Code
94704
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

Showing the most recent 10 out of 49 publications