A fast weak motif-finding algorithm based on community detection in graphs.

ABSTRACT:

Background

Identification of transcription factor binding sites (also called 'motif discovery') in DNA sequences is a basic step in understanding genetic regulation. Although many successful programs have been developed, the problem is far from being solved on account of diversity in gene expression/regulation and the low specificity of binding sites. State-of-the-art algorithms have their own constraints (e.g., high time or space complexity for finding long motifs, low precision in identification of weak motifs, or the OOPS constraint: one occurrence of the motif instance per sequence) which limit their scope of application.

Results

In this paper, we present a novel and fast algorithm we call TFBSGroup. It is based on community detection from a graph and is used to discover

SUBMITTER: Jia C 

PROVIDER: S-EPMC3726413 | biostudies-literature | 2013 Jul

REPOSITORIES: biostudies-literature