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HaploBlockFinder: haplotype block analyses

2003; Oxford University Press; Volume: 19; Issue: 10 Linguagem: Inglês

10.1093/bioinformatics/btg142

1367-4811

Kun Zhang, Jin Li,

Genetic and phenotypic traits in livestock

Abstract Summary: Recent studies have unveiled discrete block-like structures of linkage disequilibrium (LD) in the human genome. We have developed a set of computer programs to analyze the block-like LD structures (haplotype blocks) based on haplotype data. Three definitions of haplotype block are supported, including minimal LD range, no historic recombination, and chromosome coverage. Tagged SNPs that uniquely distinguish common haplotypes are identified. A greedy algorithm was used to improve the efficiency. Two separate utilities were also provided to assist visual inspection of haplotype block structure and pattern of linkage disequilibrium. Availability: A web interface for the HaploBlockFinder is available at http://cgi.uc.edu/cgi-bin/kzhang/haploBlockFinder.cgi the source codes are also freely available on the web site. Contact: jinl@ucmail.uc.edu * To whom correspondence should be addressed.