Research

Finding the region of pseudo-periodic tandem repeats in biological sequences

Xiaowen Liu and Lusheng Wang

Department of Computer Science, City University of Hong Kong, Kowloon, Hong Kong

author email corresponding author email

Algorithms for Molecular Biology 2006, 1:2doi:10.1186/1748-7188-1-2

Published:	28 February 2006

Abstract

Summary

The genomes of many species are dominated by short sequences repeated consecutively. It is estimated that over 10% of the human genome consists of tandemly repeated sequences. Finding repeated regions in long sequences is important in sequence analysis.

We develop a software, LocRepeat, that finds regions of pseudo-periodic repeats in a long sequence. We use the definition of Li et al. [1] for the pseudo-periodic partition of a region and extend the algorithm that can select the repeated region from a given long sequence and give the pseudo-periodic partition of the region.

Availability

LocRepeat is available at http://www.cs.cityu.edu.hk/~lwang/software/LocRepeat webcite