Efficient Algorithms for SNP Haplotype Block Selection Problems
COCOON '08 Proceedings of the 14th annual international conference on Computing and Combinatorics
Genotype Tagging with Limited Overfitting
BSB '09 Proceedings of the 4th Brazilian Symposium on Bioinformatics: Advances in Bioinformatics and Computational Biology
Logic based methods for SNPs tagging and reconstruction
Computers and Operations Research
Fuzzy guided BPSO method for haplotype tag SNP selection
FUZZ-IEEE'09 Proceedings of the 18th international conference on Fuzzy Systems
Efficient and accurate haplotype inference by combining parsimony and pedigree information
ANB'10 Proceedings of the 4th international conference on Algebraic and Numeric Biology
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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@usc.edu