Using suffix trees for gapped motif discovery

被引：0
|
作者：
Rocke, E [1 ]
机构：
[1] Univ Washington, CSE Dept, Seattle, WA 98195 USA
来源：
COMBINATORIAL PATTERN MATCHING | 2000年 / 1848卷
关键词：
D O I：
暂无
中图分类号：
TP301 [理论、方法];
学科分类号：
081202 ;
摘要：
Gibbs sampling is a local search method that can be used to find novel motifs in a text string. In previous work [8], we have proposed a modified Gibbs sampler that can discover novel gapped motifs of varying lengths and occurrence rates in DNA or protein sequences. The Gibbs sampling method requires repeated searching of the text for the best match to a constantly evolving collection of aligned strings, and each search pass previously required theta (nl) time, where I is the length of the motif and n the length of the original sequence. This paper presents a novel method for using suffix trees to greatly improve the performance of the Gibbs sampling approach.
引用
收藏
页码：335 / 349
页数：15
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