A 2D Pattern Matching Algorithm for Comparing Primary Protein Sequences

Guohua Huang; Weiping Huang; Wenping Xie; Yongfan Li; Lixin Xu; Houqing Zhou

doi:10.2174/1574893609666140516005556

ISSN: 1574-8936
E-ISSN: 2212-392X

A 2D Pattern Matching Algorithm for Comparing Primary Protein Sequences
By Guohua Huang, Weiping Huang, Wenping Xie, Yongfan Li, Lixin Xu and Houqing Zhou
Source: Current Bioinformatics, Volume 9, Issue 3, Jul 2014, p. 210 - 217
DOI: https://doi.org/10.2174/1574893609666140516005556
- Available online: 01 Jul 2014

Abstract

Sequence comparison in the form of alignment plays a crucial role in the area of bioinformatics. However, alignment is commonly restricted by the number of aligned sequences. To address this problem, we presented a 2D pattern matching algorithm for comparing protein sequences. The new algorithm which is an alignment-free comparison is capable of allowing fast comparison even among a large number of protein sequences. The simulation on the artificial sequences indicated that our method would be robust. And the experiment on real protein sequences showed that our method would be effective.

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2014-07-01

2025-10-15

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Article Type: Research Article

Keyword(s): Alignment; alignment-free comparison; binary tree; graphical representation; phylogenetic tree; sequence; similarity distance

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A 2D Pattern Matching Algorithm for Comparing Primary Protein Sequences

Abstract

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