CHOISS for selection of single nucleotide polymorphism markers on interval regularity.
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(n(2)) calculations and comparisons by elimination of redundancy.
Lee
Soohyun
S
Department of Biological Sciences, Korea Advanced Institute of Science and Technology, 373-1 Guseong-dong, Yuseong-gu, Daejeon 305-701, Korea.
Kang
Changwon
C
D000465:Algorithms; D020869:Gene Expression Profiling / Q000379:methods*; D005819:Genetic Markers / Q000235:genetics*; D008957:Models, Genetic; D015233:Models, Statistical; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*; D016415:Sequence Alignment / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software
D005819:Genetic Markers