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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Series: | Mathematical Problems in Engineering |
Online Access: | http://dx.doi.org/10.1155/2012/490649 |
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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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