Project Number: 1265-31000-098-04
Project Type: Specific Cooperative Agreement

Start Date: Jan 18, 2008
End Date: Dec 31, 2009

Objective:
The objective of this cooperative research project is to design tools to process and analyze DNA sequence data, including characterization of genome structural variations such as segmental duplication and copy number variations (CNV).

Approach:
Software will be developed and adapted for analyzing 1) the extent and pattern of segmental duplication in the cattle genome assembly and 2) the whole genome structure variation data being generated by the CNV project sponsored by USDA, including use of array comparative genomic hybridization (array CGH) information, survey of normal baselines of CNV and identification of positional candidate genes. Emphasis should be given to problems related to the bovine genome sequencing and hapmap projects, as BFGL closely involved in those efforts, although development of tools with wide utility is a priority. Tools will be developed or adapted to reliably identify and characterize CNV across and within breeds or strains of a species.