A tag SNPs selection and reconstruction algorithm

Computer Engineering & Science

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A tag SNPs selection and reconstruction algorithm

ZHAO Jing1,WEI Bin2

（1.School of Control Engineering,Xijing University,Xi’an 710123;

2.Department of Electronic Technique,Armed Police Engineering University,Xi’an

710086,China）

Received:2015-09-18 Revised:2015-10-27 Online:2016-11-25 Published:2016-11-25

Abstract

Abstract:

Obtaining the association between complex diseases and single nucleotide polymorphisms

(SNPs) is one of the most important tasks of bioinformatics.However,the huge spending

limits its development and applications,selecting a set of tag SNPs therefore becomes an

important step to reduce the cost for association study.Recently,some algorithms have been

proposed for solving this problem,but most of them cannot meet the requirements of

practical applications in terms of accuracy level and number of tags.We introduce a new

method which uses an improved particle swarm optimization algorithm to predict the nontag

SNPs,and employ an novel forwardmatrix method to select tag SNPs.To measure the quality

of the correction rate and the number of tag SNPs,we utilize several databases to test our

method,and we also compare it with other methods.The results show that the proposed method

can effectively enhance the tag SNPs prediction in terms of accuracy and a smaller subset

of tag SNPs.

Key words: single nucleotide polymorphism, tag, particle swarm optimization

ZHAO Jing1,WEI Bin2.

A tag SNPs selection and reconstruction algorithm

[J]. Computer Engineering & Science.

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A tag SNPs selection and reconstruction algorithm

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