Current Bioinformatics

Alessandro Giuliani
Istituto Superiore di Sanitá (Italian NIH) Environment and Health Dept
Roma
Italy

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A 2D Pattern Matching Algorithm for Comparing Primary Protein Sequences

Author(s): Guohua Huang, Weiping Huang, Wenping Xie, Yongfan Li, Lixin Xu and Houqing Zhou

Affiliation: Department of Mathematics, Shaoyang University, Shaoyang, Hunan 422000, China.

Keywords: Alignment, alignment-free comparison, binary tree, graphical representation, phylogenetic tree, sequence, similarity distance.

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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Article Details

VOLUME: 9
ISSUE: 3
Page: [210 - 217]
Pages: 8
DOI: 10.2174/1574893609666140516005556