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

Algorithms for Molecular Biology BioMedCentral Research Open Access Finding the region of pseudo-periodic tandem repeats in biological sequences Xiaowen Liu* and Lusheng Wang* Address: Department of Computer Science, City University of Hong Kong, Kowloon, Hong Kong Email: Xiaowen Liu* - liuxw@.hk; Lusheng Wang* - lwang@.hk * Corresponding authors Published: 28 February 2006 Received: 23 February 2006 Accepted: 28 February 2006 Algorithms for Molecular Biology2006, 1:2 doi:10.1186/1748-7188-1-2 This article is available from: /content/1/1/2 ? 2006Liu and Wang; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. 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 .hk/~lwang/software/LocRepeat Background This tandem repeat consists of 35 approximate copies of the repeated pattern CCT. Finding pseudo-periodic repeats (or tandem repeats) is an important task in biological sequence analysis [1-3]. 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. About 10–25% of