An Improved Scoring Matrix for Multiple Sequence Alignment

An Improved Scoring Matrix for Multiple Sequence Alignment

The way for performing multiple sequence alignment is based on the criterion of the maximum-scored information content computed from a weight matrix, but it is possible to have two or more alignments to have the same highest score leading to ambiguities in selecting the best alignment. This paper ad...

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Main Authors: Jian-Jun Shu, Kian Yan Yong, Weng Kong Chan
Format: Article
Language:English
Published: Hindawi Limited 2012-01-01
Series:Mathematical Problems in Engineering
Online Access:http://dx.doi.org/10.1155/2012/490649
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spelling doaj-a6002dc9e89f43f6a3ed4d2508a4e34e2020-11-24T22:28:54ZengHindawi LimitedMathematical Problems in Engineering1024-123X1563-51472012-01-01201210.1155/2012/490649490649An Improved Scoring Matrix for Multiple Sequence AlignmentJian-Jun Shu0Kian Yan Yong1Weng Kong Chan2School of Mechanical & Aerospace Engineering, Nanyang Technological University, 50 Nanyang Avenue, 639798, SingaporeSchool of Mechanical & Aerospace Engineering, Nanyang Technological University, 50 Nanyang Avenue, 639798, SingaporeSchool of Mechanical & Aerospace Engineering, Nanyang Technological University, 50 Nanyang Avenue, 639798, SingaporeThe way for performing multiple sequence alignment is based on the criterion of the maximum-scored information content computed from a weight matrix, but it is possible to have two or more alignments to have the same highest score leading to ambiguities in selecting the best alignment. This paper addresses this issue by introducing the concept of joint weight matrix to eliminate the randomness in selecting the best multiple sequence alignment. Alignments with equal scores are iteratively rescored with the joint weight matrix of increasing level (nucleotide pairs, triplets, and so on) until one single best alignment is eventually found. This method for resolving ambiguity in multiple sequence alignment can be easily implemented by use of the improved scoring matrix.http://dx.doi.org/10.1155/2012/490649
collection DOAJ
language English
format Article
sources DOAJ
author Jian-Jun Shu
Kian Yan Yong
Weng Kong Chan
spellingShingle Jian-Jun Shu
Kian Yan Yong
Weng Kong Chan
An Improved Scoring Matrix for Multiple Sequence Alignment
Mathematical Problems in Engineering
author_facet Jian-Jun Shu
Kian Yan Yong
Weng Kong Chan
author_sort Jian-Jun Shu
title An Improved Scoring Matrix for Multiple Sequence Alignment
title_short An Improved Scoring Matrix for Multiple Sequence Alignment
title_full An Improved Scoring Matrix for Multiple Sequence Alignment
title_fullStr An Improved Scoring Matrix for Multiple Sequence Alignment
title_full_unstemmed An Improved Scoring Matrix for Multiple Sequence Alignment
title_sort improved scoring matrix for multiple sequence alignment
publisher Hindawi Limited
series Mathematical Problems in Engineering
issn 1024-123X
1563-5147
publishDate 2012-01-01
description The way for performing multiple sequence alignment is based on the criterion of the maximum-scored information content computed from a weight matrix, but it is possible to have two or more alignments to have the same highest score leading to ambiguities in selecting the best alignment. This paper addresses this issue by introducing the concept of joint weight matrix to eliminate the randomness in selecting the best multiple sequence alignment. Alignments with equal scores are iteratively rescored with the joint weight matrix of increasing level (nucleotide pairs, triplets, and so on) until one single best alignment is eventually found. This method for resolving ambiguity in multiple sequence alignment can be easily implemented by use of the improved scoring matrix.
url http://dx.doi.org/10.1155/2012/490649
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AT kianyanyong improvedscoringmatrixformultiplesequencealignment
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