Lecture notes in computer science : multiple DNA sequence alignment using joint weight matrix

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...

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Main Authors: Shu, Jian Jun, Yong, Kian Yan, Chan, Weng Kong
Other Authors: School of Mechanical and Aerospace Engineering
Format: Conference or Workshop Item
Language:English
Published: 2011
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Online Access:https://hdl.handle.net/10356/93996
http://hdl.handle.net/10220/7188
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Institution: Nanyang Technological University
Language: English
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spelling sg-ntu-dr.10356-939962023-03-04T17:07:18Z Lecture notes in computer science : multiple DNA sequence alignment using joint weight matrix Shu, Jian Jun Yong, Kian Yan Chan, Weng Kong School of Mechanical and Aerospace Engineering International Conference on Computational Science and Its Applications (11th : 2011 : Santander, Spain) DRNTU::Engineering::Computer science and engineering::Computer applications::Life and medical sciences 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 alignment of multiple sequences. Alignments with equal scores are iteratively re-scored with joint weight matrix of increasing level (nucleotide pairs, triplets and so on) until one single best alignment is eventually found. This method can be easily implemented to algorithms using weight matrix for scoring such as those based on the widely used Gibbs sampling method. Accepted version 2011-10-10T05:16:23Z 2019-12-06T18:48:54Z 2011-10-10T05:16:23Z 2019-12-06T18:48:54Z 2011 2011 Conference Paper Shu, J. J., Yong, K. Y., & Chan, W. K. (2011). Lecture notes in computer science: Multiple DNA sequence alignment using joint weight matrix. International Conference on Computational Science and Its Applications (11th:2011:Santander). https://hdl.handle.net/10356/93996 http://hdl.handle.net/10220/7188 10.1007/978-3-642-21931-3_51 161332 en © 2011 Springer-Verlag Berlin Heidelberg. This is the author created version of a work that has been peer reviewed and accepted for publication by Computational Science and Its Applications - ICCSA 2011, Springer-Verlag Berlin Heidelberg. It incorporates referee’s comments but changes resulting from the publishing process, such as copyediting, structural formatting, may not be reflected in this document. The published version is available at: [DOI: http://dx.doi.org/10.1007/978-3-642-21931-3_51]. 8 p. application/pdf
institution Nanyang Technological University
building NTU Library
continent Asia
country Singapore
Singapore
content_provider NTU Library
collection DR-NTU
language English
topic DRNTU::Engineering::Computer science and engineering::Computer applications::Life and medical sciences
spellingShingle DRNTU::Engineering::Computer science and engineering::Computer applications::Life and medical sciences
Shu, Jian Jun
Yong, Kian Yan
Chan, Weng Kong
Lecture notes in computer science : multiple DNA sequence alignment using joint weight matrix
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 alignment of multiple sequences. Alignments with equal scores are iteratively re-scored with joint weight matrix of increasing level (nucleotide pairs, triplets and so on) until one single best alignment is eventually found. This method can be easily implemented to algorithms using weight matrix for scoring such as those based on the widely used Gibbs sampling method.
author2 School of Mechanical and Aerospace Engineering
author_facet School of Mechanical and Aerospace Engineering
Shu, Jian Jun
Yong, Kian Yan
Chan, Weng Kong
format Conference or Workshop Item
author Shu, Jian Jun
Yong, Kian Yan
Chan, Weng Kong
author_sort Shu, Jian Jun
title Lecture notes in computer science : multiple DNA sequence alignment using joint weight matrix
title_short Lecture notes in computer science : multiple DNA sequence alignment using joint weight matrix
title_full Lecture notes in computer science : multiple DNA sequence alignment using joint weight matrix
title_fullStr Lecture notes in computer science : multiple DNA sequence alignment using joint weight matrix
title_full_unstemmed Lecture notes in computer science : multiple DNA sequence alignment using joint weight matrix
title_sort lecture notes in computer science : multiple dna sequence alignment using joint weight matrix
publishDate 2011
url https://hdl.handle.net/10356/93996
http://hdl.handle.net/10220/7188
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