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Bioinformatics Advance Access published online on February 5, 2004
Bioinformatics, doi:10.1093/bioinformatics/btg458
Bioinformatics © Oxford University Press 2004; all rights reserved
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Received October 2, 2003
Accepted October 2, 2003

Applications note

CHOISS for selection of single nucleotide polymorphism markers on interval regularity

Soohyun Lee 1 Changwon Kang 1*

1 Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 305-701, Korea

* To whom correspondence should be addressed. E-mail: ckang{at}kaist.ac.kr.


  Abstract

Summary: We developed algorithms that find a set of SNP markers based on interval regularity, given either the number of SNPs to choose (m) or the desired interval (I), subject to minimum variance or minimum sum of squared deviations from I. In both cases, the number of all possible sets increases exponentially with respect to the number of input SNPs (n), but our algorithms find the minima only with O(n2) calculations and comparisons by elimination of redundancy.

Availability: A Windows executable program CHOISS is freely available at http://biochem.kaist.ac.kr/choiss.htm.

Supplementary information: http://biochem.kaist.ac.kr/choiss.htm.


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