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Bioinformatics Advance Access originally published online on February 5, 2004
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Bioinformatics 20(4) © Oxford University Press 2004; all rights reserved.

Applications Note

CHOISS for selection of single nucleotide polymorphism markers on interval regularity

Soohyun Lee and Changwon Kang *

Department of Biological Sciences, Korea Advanced Institute of Science and Technology, 373-1 Guseong-dong, Yuseong-gu, Daejeon 305-701, Korea

Received on August 18, 2003 ; accepted on October 2, 2003
Advance Access Publication January 22, 2004

Summary: We developed algorithms that find a set of single nucleotide polymorphism (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

Contact: ckang{at}kaist.ac.kr

* To whom correspondence should be addressed.


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