Research
Finding the region of pseudo-periodic tandem repeats in biological sequences
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Corresponding authors: Xiaowen Liu liuxw@cs.cityu.edu.hk - Lusheng Wang lwang@cs.cityu.edu.hk
Department of Computer Science, City University of Hong Kong, Kowloon, Hong Kong
Algorithms for Molecular Biology 2006, 1:2 doi:10.1186/1748-7188-1-2
Published: 28 February 2006Abstract
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