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A DNA based Approach to find Closed Repetitive Gapped Subsequences from a Sequence Database

by B.Lavanya, A.Murugan
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International Journal of Computer Applications
Foundation of Computer Science (FCS), NY, USA
Volume 29 - Number 5
Year of Publication: 2011
Authors: B.Lavanya, A.Murugan
10.5120/3558-4893

B.Lavanya, A.Murugan . A DNA based Approach to find Closed Repetitive Gapped Subsequences from a Sequence Database. International Journal of Computer Applications. 29, 5 ( September 2011), 45-49. DOI=10.5120/3558-4893

@article{ 10.5120/3558-4893,
author = { B.Lavanya, A.Murugan },
title = { A DNA based Approach to find Closed Repetitive Gapped Subsequences from a Sequence Database },
journal = { International Journal of Computer Applications },
issue_date = { September 2011 },
volume = { 29 },
number = { 5 },
month = { September },
year = { 2011 },
issn = { 0975-8887 },
pages = { 45-49 },
numpages = {9},
url = { https://ijcaonline.org/archives/volume29/number5/3558-4893/ },
doi = { 10.5120/3558-4893 },
publisher = {Foundation of Computer Science (FCS), NY, USA},
address = {New York, USA}
}
%0 Journal Article
%1 2024-02-06T20:15:02.279731+05:30
%A B.Lavanya
%A A.Murugan
%T A DNA based Approach to find Closed Repetitive Gapped Subsequences from a Sequence Database
%J International Journal of Computer Applications
%@ 0975-8887
%V 29
%N 5
%P 45-49
%D 2011
%I Foundation of Computer Science (FCS), NY, USA
Abstract

In bioinformatics, the discovery of transcription factor binding affinities is important. This is done by sequence analysis of micro array data. The determination of continuous and gapped motifs accurately from the given long sequence of data, say genetic data is challenging and requires a detailed study. In this paper, we propose an algorithm that can be used for finding short continuous, short gapped, long continuous, long gapped and negative existence of motifs. We propose a new DNA algorithmic approach which solves the accurate determination of motifs both continuous and gapped, parallely with optimum time. Using the proposed algorithm, firstly a modified Position Weight Matrix is generated according to the searched motif pattern, which contains the position of its appearance in the given database, using DNA operations. Then, this Position Weight Matrix is used for searching of continuous and gapped subsequences. The proposed algorithm can be used to search genetic, scientific as well as commercial databases. Implementation results shown the correctness of the algorithm. Finally, the validity of the algorithm is checked and its complexity is analyzed.

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Index Terms

Computer Science
Information Sciences

Keywords

DNA computation DNA operations Motifs PWM

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