Finding Motifs in DNA Sequences Using Low-Dispersion Sequences

被引：49

作者：

Wang, Xun ^{[1
]}

Miao, Ying ^{[1
]}

Cheng, Minquan ^{[2
]}

机构：

[1] Univ Tsukuba, Grad Sch Syst & Informat Engn, Tsukuba, Ibaraki 3058577, Japan

[2] Guangxi Normal Univ, Dept Math, Guilin, Peoples R China

来源：

JOURNAL OF COMPUTATIONAL BIOLOGY | 2014年 / 21卷 / 04期

基金：

美国国家科学基金会;

关键词：

random projection; developed almost difference family; uniform projection; motif finding; low-dispersion sequence; EXPECTATION MAXIMIZATION; PROJECTION; DISCOVERY; BINDING;

D O I：

10.1089/cmb.2013.0054

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

Motif finding problems, abstracted as the planted (l, d)-motif finding problem, are a major task in molecular biology-finding functioning units and genes. In 2002, the random projection algorithm was introduced to solve the challenging (15, 4)-motif finding problem by using randomly chosen templates. Two years later, a so-called uniform projection algorithm was developed to improve the random projection algorithm by means of low-dispersion sequences generated by coverings. In this article, we introduce an improved projection algorithm called the low-dispersion projection algorithm, which uses low-dispersion sequences generated by developed almost difference families. Compared with the random projection algorithm, the low-dispersion projection algorithm can solve the (l, d)-motif finding problem with fewer templates without decreasing the success rate.

引用

页码：320 / 329

页数：10

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