htSNPer1.0: software for haplotype block partition and htSNPs selection. Results: A heuristic algorithm, generalized branch-and-bound algorithm, is applied to the searching of minimal set of haplotype tagging SNPs (htSNPs) according to different htSNPs performance criteria. We develop a software htSNPer1.0 to implement the algorithm, and integrate three htSNPs performance criteria and four haplotype block definitions for haplotype block partitioning. It is a software with powerful Graphical User Interface (GUI), which can be used to characterize the haplotype block structure and select htSNPs in the candidate gene or interested genomic regions. It can find the global optimization with only a fraction of the computing time consumed by exhaustive searching algorithm. Conclusion: htSNPer1.0 allows molecular geneticists to perform haplotype block analysis and htSNPs selection using different definitions and performance criteria. The software is a powerful tool for those focusing on association mapping based on strategy of haplotype block and htSNPs.
References in zbMATH (referenced in 2 articles )
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- Zahiri, J.; Mahdevar, G.; Nowzari-dalini, A.; Ahrabian, H.; Sadeghi, M.: A novel efficient dynamic programming algorithm for haplotype block partitioning (2010)
- Katanforoush, Ali; Sadeghi, Mehdi; Pezeshk, Hamid; Elahi, Elahe: Global haplotype partitioning for maximal associated SNP pairs (2009) ioport