A 2D Pattern Matching Algorithm for Comparing Primary Protein Sequences

Title:A 2D Pattern Matching Algorithm for Comparing Primary Protein Sequences

Volume: 9 Issue: 3

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

Affiliation:

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.

Cite this article as:

Huang Guohua, Huang Weiping, Xie Wenping, Li Yongfan, Xu Lixin and Zhou Houqing, A 2D Pattern Matching Algorithm for Comparing Primary Protein Sequences, Current Bioinformatics 2014; 9 (3) . https://dx.doi.org/10.2174/1574893609666140516005556