A Novel Markov Pairwise Protein Sequence Alignment Method for Sequence 665 Comparison

Authors: Zhao, Xing-Ming; Cheung, Yiu-Ming; Huang, De-Shuang

Source: Protein and Peptide Letters, Volume 12, Number 7, October 2005 , pp. 665-669(5)

Publisher: Bentham Science Publishers

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Abstract:

The Smith-Waterman (SW) algorithm is a typical technique for local sequence alignment in computational biology. However, the SW algorithm does not consider the local behaviours of the amino acids, which may result in loss of some useful information. Inspired by the success of Markov Edit Distance (MED) method, this paper therefore proposes a novel Markov pairwise protein sequence alignment (MPPSA) method that takes the local context dependencies into consideration. The numerical results have shown its superiority to the SW for pairwise protein sequence comparison.

Keywords: protein sequence comparison; markov pairwise protein sequence alignment (mppsa); markov random filed; dynamic programming

Document Type: Review article

Affiliations: 1: Intelligent Computing Lab, Hefei Institute of Intelligent Machines, Chinese Academy of Sciences, P.O.Box 1130, Hefei, Anhui, 230031, China;

Publication date: 2005-10-01

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Protein & Peptide Letters publishes short papers in all important aspects of protein and peptide research, including structural studies, recombinant expression, function, synthesis, enzymology, immunology, molecular modeling, drug design etc. Manuscripts must have a significant element of novelty, timeliness and urgency that merit rapid publication. Reports of crystallisation, and preliminary structure determinations of biologically important proteins are acceptable. Purely theoretical papers are also acceptable provided they provide new insight into the principles of protein/peptide structure and function.