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

Authors:
Jian-Jun Shu;Kian Yan Yong;Weng Kong Chan
Affiliations:
School of Mechanical & Aerospace Engineering, Nanyang Technological University, Singapore;School of Mechanical & Aerospace Engineering, Nanyang Technological University, Singapore;School of Mechanical & Aerospace Engineering, Nanyang Technological University, Singapore
Venue:
ICCSA'11 Proceedings of the 2011 international conference on Computational science and its applications - Volume Part III
Year:
2011

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Abstract

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.