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Bioinformatics Vol. 19 no. 10 2003
Pages 1300-1301
© 2003 Oxford University Press

Applications Note

HaploBlockFinder: haplotype block analyses

Kun Zhang and Li Jin *

Center for Genome Information, Department of Environmental Health, University of Cincinnati, Cincinnati, OH 45267, USA

Received on September 16, 2002 ; revised on November 17, 2002 ; accepted on January 25, 2003

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{at}ucmail.uc.edu

* To whom correspondence should be addressed.


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