Genetic algorithm for dyad pattern finding in DNA sequences

被引：14

作者：

Zare-Mirakabad, Fatemeh ^{[1
]}

Ahrabian, Hayedeh ^{[1
,2
]}

Sadeghi, Mehdi ^{[3
,4
]}

Hashemifar, Somaieh ^{[2
]}

Nowzari-Dalini, Abbas ^{[1
,2
]}

Goliaei, Bahram ^{[1
]}

机构：

[1] Univ Tehran, Inst Biochem & Biophys, Dept Bioinformat, Tehran, Iran

[2] Univ Tehran, Sch Math Stat & Comp Sci, Ctr Excellence Biomath, Tehran, Iran

[3] Natl Inst Genet Engendering & Biotechnol, Tehran, Iran

[4] Inst Studies Theoret Phys & Math IPM, Sch Comp Sci, Tehran, Iran

来源：

GENES & GENETIC SYSTEMS | 2009年 / 84卷 / 01期

关键词：

dyad pattern; genetic algorithm; motif finding; REGULATORY ELEMENTS; BINDING SITES; DISCOVERY; MOTIFS; IDENTIFICATION; PROMOTER;

D O I：

10.1266/ggs.84.81

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

In this paper a novel genetic algorithm is presented for the dyad motif finding problem. The genetic algorithm uses a multi-objective fitness function based on the sum of pairs, the number of matches, and the information content. The individuals required for the population pool in the genetic algorithm are optimized by Gibbs sampling method. Also, new crossover and mutation operators are designed. The algorithm is implemented and tested on the different types of real datasets. The results are compared with other well-known algorithms and the effectiveness of our algorithm is shown.

引用

页码：81 / 93

页数：13

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