A novel Markov pairwise protein sequence alignment method for sequence comparison

Xing Ming Zhao, Yiu Ming CHEUNG, De Shuang Huang*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

2 Citations (Scopus)

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.

Original languageEnglish
Pages (from-to)665-669
Number of pages5
JournalProtein and Peptide Letters
Volume12
Issue number7
DOIs
Publication statusPublished - Oct 2005

Scopus Subject Areas

  • Structural Biology
  • Biochemistry

User-Defined Keywords

  • Dynamic Programming
  • Markov Pairwise Protein Sequence Alignment (MPPSA)
  • Markov Random Filed
  • Protein Sequence Comparison

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