论文信息 - HaploBlockFinder: Haplotype Block Analyses

HaploBlockFinder: Haplotype Block Analyses

UNLABELLED 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.

Kun Zhang | Li Jin | Li Jin | Kun Zhang

[1] Lon R. Cardon,et al. A first-generation linkage disequilibrium map of human chromosome 22 , 2002, Nature.

[2] S. P. Fodor,et al. Blocks of Limited Haplotype Diversity Revealed by High-Resolution Scanning of Human Chromosome 21 , 2001, Science.

[3] S. Gabriel,et al. The Structure of Haplotype Blocks in the Human Genome , 2002, Science.

[4] M. Daly,et al. High-resolution haplotype structure in the human genome , 2001, Nature Genetics.

[5] M. Waterman,et al. A dynamic programming algorithm for haplotype block partitioning , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[6] J. Akey,et al. Distribution of recombination crossovers and the origin of haplotype blocks: the interplay of population history, recombination, and mutation. , 2002, American journal of human genetics.

[7] Lukas Wagner,et al. A Greedy Algorithm for Aligning DNA Sequences , 2000, J. Comput. Biol..

[8] D. Goldstein. Islands of linkage disequilibrium , 2001, Nature Genetics.

[9] A. Jeffreys,et al. Intensely punctate meiotic recombination in the class II region of the major histocompatibility complex , 2001, Nature Genetics.

[10] Pardis C Sabeti,et al. Linkage disequilibrium in the human genome , 2001, Nature.