A novel method for similarity/dissimilarity analysis of protein sequences

被引：16

作者：

Mu, Zengchao ^{[1
]}

Wu, Jing ^{[1
]}

Zhang, Yusen ^{[1
]}

机构：

[1] Shandong Univ Weihai, Sch Math & Stat, Weihai 264209, Peoples R China

来源：

PHYSICA A-STATISTICAL MECHANICS AND ITS APPLICATIONS | 2013年 / 392卷 / 24期

关键词：

Protein sequence; Similarity; Distance frequency matrix; Phylogenetic tree; AMINO-ACID-COMPOSITION; SUPPORT VECTOR MACHINE; GRAPHICAL REPRESENTATION; SUBCELLULAR LOCATION; STRUCTURAL CLASS; DNA-SEQUENCES; SIMILARITY ANALYSIS; PREDICTION; PAIRS; LOCALIZATION;

D O I：

10.1016/j.physa.2013.08.008

中图分类号：

O4 [物理学];

学科分类号：

0702 ;

摘要：

Sequence comparison is one of the major tasks in bioinformatics, which can be used to study structural and functional conservation, as well as evolutionary relations among the sequences. In this paper, we introduce the concept of distance frequency of amino acid pairs and propose a new numerical characterization of protein sequences, which converts any protein sequence into a distance frequency matrix. Using this distance frequency matrix, we can compare the similarity of protein sequences. In order to confirm the validity of our method, we test it with two experiments. The results show that our method is effective. (C) 2013 Elsevier B.V. All rights reserved.

引用

页码：6361 / 6366

页数：6

共 37 条

[1] Abo-Elkhier M. M., 2012, J BIOPHYS CHEM, V3, P142
[2] Prediction of protein structural class using novel evolutionary collocation-based sequence representation
Chen, Ke
Kurgan, Lukasz A.
Ruan, Jishou
[J]. JOURNAL OF COMPUTATIONAL CHEMISTRY, 2008, 29 (10) : 1596 - 1604
[3] Prediction of flexible/rigid regions from protein sequences using k-spaced amino acid pairs
Chen, Ke
Kurgan, Lukasz A.
Ruan, Jishou
[J]. BMC STRUCTURAL BIOLOGY, 2007, 7
[4] Prediction of protein crystallization using collocation of amino acid pairs
Chen, Ke
Kurgan, Lukasz
Rahbari, Mandana
[J]. BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS, 2007, 355 (03) : 764 - 769
[5] Prediction of Integral Membrane Protein Type by Collocated Hydrophobic Amino Acid Pair
Chen, Ke
Jiang, Yingfu
Du, Li
Kurgan, Lukasz
[J]. JOURNAL OF COMPUTATIONAL CHEMISTRY, 2009, 30 (01) : 163 - 172
[6] Chen W, 2009, MATCH-COMMUN MATH CO, V61, P781
[7] Prediction of mucin-type O-glycosylation sites in mammalian proteins using the composition of k-spaced amino acid pairs
Chen, Yong-Zi
Tang, Yu-Rong
Sheng, Zhi-Ya
Zhang, Ziding
[J]. BMC BIOINFORMATICS, 2008, 9 (1) : 101
[8] Protein subcellular location prediction
Chou, KC
Elrod, DW
[J]. PROTEIN ENGINEERING, 1999, 12 (02): : 107 - 118
[9] Prediction of protein cellular attributes using pseudo-amino acid composition
Chou, KC
[J]. PROTEINS-STRUCTURE FUNCTION AND GENETICS, 2001, 43 (03): : 246 - 255
[10] Comparison study on k-word statistical measures for protein: From sequence to 'sequence space'
Dai, Qi
Wang, Tianming
[J]. BMC BIOINFORMATICS, 2008, 9 (1)

← 1 2 3 4 →