A 2D Pattern Matching Algorithm for Comparing Primary Protein Sequences

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

Journal Name:Current Bioinformatics

Volume 9 , Issue 3 , 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.

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

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Article Details

VOLUME: 9
ISSUE: 3
Year: 2014
Page: [210 - 217]
Pages: 8
DOI: 10.2174/1574893609666140516005556
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