2012 Annual Report 1a.Objectives (from AD-416): 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). 1b.Approach (from AD-416): 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 is 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. 3.Progress Report: During FY 2012, we interviewed and hired a postdoctoral associate for this agreement. This research also supported two objectives of its related in-house project to develop biological resources and computational tools to enhance characterization of the bovine genome sequence (Objective. 1)and to characterize conserved genome elements and identify functional genetic variation (Objective 3). These objectives directly impact Component 2 – Problem Statements A, B, and C of the National Program Action Plan. This agreement did not support any published journal articles this year.