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Bioinformatics Advance Access originally published online on August 27, 2004
Bioinformatics 2005 21(1):131-134; doi:10.1093/bioinformatics/bth482
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Bioinformatics vol. 21 issue 1 © Oxford University Press 2005; all rights reserved.

HapBlock: haplotype block partitioning and tag SNP selection software using a set of dynamic programming algorithms

Kui Zhang 1, Zhaohui Qin 2, Ting Chen 3, Jun S. Liu 4, Michael S. Waterman 3 and Fengzhu Sun 3,*

1 Section on Statistical Genetics, Department of Biostatistics, University of Alabama at Birmingham Birmingham, AL 35294, USA
2 Center for Statistical Genetics, Department of Biostatistics, University of Michigan Ann Arbor, MI 48109, USA
3 Molecular and Computational Biology Program, Department of Biological Sciences, University of Southern California 1042 W. 36th Place DRB-288, Los Angeles, CA 90089–1113, USA
4 Department of Statistics, Harvard University Cambridge, MA 02138, USA

*To whom correspondence should be addressed.

Summary: Recent studies have revealed that linkage disequilibrium (LD) patterns vary across the human genome with some regions of high LD interspersed with regions of low LD. Such LD patterns make it possible to select a set of single nucleotide polymorphism (SNPs; tag SNPs) for genome-wide association studies. We have developed a suite of computer programs to analyze the block-like LD patterns and to select the corresponding tag SNPs. Compared to other programs for haplotype block partitioning and tag SNP selection, our program has several notable features. First, the dynamic programming algorithms implemented are guaranteed to find the block partition with minimum number of tag SNPs for the given criteria of blocks and tag SNPs. Second, both haplotype data and genotype data from unrelated individuals and/or from general pedigrees can be analyzed. Third, several existing measures/criteria for haplotype block partitioning and tag SNP selection have been implemented in the program. Finally, the programs provide flexibility to include specific SNPs (e.g. non-synonymous SNPs) as tag SNPs.

Availability: The HapBlock program and its supplemental documents can be downloaded from the website http://www.cmb.usc.edu/~msms/HapBlock

Contact: fsun{at}usc.edu

Received on June 1, 2004; revised on July 20, 2004; accepted on August 11, 2004

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