Virtual mapping of cattle SNPs to human genome for alignment to bovine QTLs

Zhi-Liang Hu

Department of Animal Science, Center for Integrated Animal Genomics, Iowa State University, 2255 Kildee Hall, Ames, Iowa 50011-3150, USA

ABSTRACT: There are over 2,227,098 cattle SNPs deposited in the NCBI dbSNP database, each SNP is flanked with 250 bases sequences on both sides. For the virtual mapping, all the cattle SNP flanking sequences were downloaded and blasted against human genome with a BLAST threshold of E-value < 1E-5, Alignment length > 100 bases, and an acceptable Identity > 80%. Up to date, a total of 65,837 significant blast matches were obtained, and the represented SNPs were subsequently aligned with bovine QTL maps via the cattle-human RH comparative map (Everts-van der Wind et al., 2005) built in the Cattle QTLdb.

STATUS: In progress.