Large-scale motif discovery using DNA Gray code and equiprobable oligomers.

ABSTRACT:

Motivation

How to find motifs from genome-scale functional sequences, such as all the promoters in a genome, is a challenging problem. Word-based methods count the occurrences of oligomers to detect excessively represented ones. This approach is known to be fast and accurate compared with other methods. However, two problems have hampered the application of such methods to large-scale data. One is the computational cost necessary for clustering similar oligomers, and the other is the bias in the frequency of fixed-length oligomers, which complicates the detection of significant words.

Results

We introduce a method that uses a DNA Gray code and equiprobable oligomers, which solve the clustering problem and the oligomer bias, respectively. Our method can analyze 18 000 sequenc

SUBMITTER: Ichinose N 

PROVIDER: S-EPMC3244767 | biostudies-literature | 2012 Jan

REPOSITORIES: biostudies-literature