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Efficient Algorithm for Extracting Complete Repeats from Biological Sequences

by Munina Yusufu, Gulina Yusufu
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International Journal of Computer Applications
Foundation of Computer Science (FCS), NY, USA
Volume 128 - Number 16
Year of Publication: 2015
Authors: Munina Yusufu, Gulina Yusufu
10.5120/ijca2015906752

Munina Yusufu, Gulina Yusufu . Efficient Algorithm for Extracting Complete Repeats from Biological Sequences. International Journal of Computer Applications. 128, 16 ( October 2015), 33-37. DOI=10.5120/ijca2015906752

@article{ 10.5120/ijca2015906752,
author = { Munina Yusufu, Gulina Yusufu },
title = { Efficient Algorithm for Extracting Complete Repeats from Biological Sequences },
journal = { International Journal of Computer Applications },
issue_date = { October 2015 },
volume = { 128 },
number = { 16 },
month = { October },
year = { 2015 },
issn = { 0975-8887 },
pages = { 33-37 },
numpages = {9},
url = { https://ijcaonline.org/archives/volume128/number16/22960-2015906752/ },
doi = { 10.5120/ijca2015906752 },
publisher = {Foundation of Computer Science (FCS), NY, USA},
address = {New York, USA}
}
%0 Journal Article
%1 2024-02-06T23:21:54.760501+05:30
%A Munina Yusufu
%A Gulina Yusufu
%T Efficient Algorithm for Extracting Complete Repeats from Biological Sequences
%J International Journal of Computer Applications
%@ 0975-8887
%V 128
%N 16
%P 33-37
%D 2015
%I Foundation of Computer Science (FCS), NY, USA
Abstract

In this paper, an approach for efficiently extracting the repeating patterns in a biological sequence is proposed. A repeating pattern is a subsequence which appears more than once in a sequence, which is one of the most important features that can be used for revealing functional or evolutionary relationships in biological sequences. The algorithm does a rapid scan of the string to find repeating regions where the repeating substring has been marked using length, occurrence positions, and occurrence frequency. The algorithm execute in linear time and space independent of alphabet size. The algorithm also has the capability to restrict output complete repeats in which length (period) p ≥ pmin, where pmin ≥ 1 is a user-specified minimum. The algorithm outputs complete repeats, and can be extended or applied to other situations, for example computing maximal repeats, or finding common motifs in a set of biological sequences.

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Index Terms

Computer Science
Information Sciences

Keywords

Complete repeats Biological sequence Suffix array Motif finding

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