Chaos Game Representation for Discriminating Thermophilic from Mesophilic Protein Sequences

Author

Hu, Xue-Hai ; Xia, Jing-Bo ; Niu, Xiao-Hui ; Ma, Xuan ; Song, Chao-Hong ; Shi, Feng

Author_Institution

Coll. of Sci., Huazhong Agric. Univ., Wuhan, China

fYear

2009

fDate

11-13 June 2009

Firstpage

1

Lastpage

4

Abstract

Can sequence analysis tell us about the function of protein? A basic question in protein science is which kind of proteins extent thermostability. Chaos game representation (CGR) can investigate the patterns hiding in protein sequence, visually revealing previously unknown structure. In this paper, we convert every protein sequence into a 20-dimensional vector by CGR algorithm, and based on these vectors we discriminate thermophiles from mesophiles using support vector machine (SVM). The overall accuracy achieves 100% in resubstitution test, and 87.12% in Jackknife test. Moreover, Matthews correlation coefficients (MCC) is 0.745.

Keywords

biology computing; biothermics; correlation methods; game theory; proteins; sequences; statistical testing; support vector machines; thermal stability; vectors; 20-dimensional vector; Jackknife test; Matthews correlation coefficients; SVM; chaos game representation; hiding pattern; mesophilic protein sequences; resubstitution test; support vector machine; thermophilic discrimination; thermostability; Amino acids; Bonding; Chaos; DNA; Educational institutions; Microorganisms; Organisms; Protein sequence; Support vector machines; Testing;

fLanguage

English

Publisher

ieee

Conference_Titel

Bioinformatics and Biomedical Engineering , 2009. ICBBE 2009. 3rd International Conference on

Conference_Location

Beijing

Print_ISBN

978-1-4244-2901-1

Electronic_ISBN

978-1-4244-2902-8

Type

conf

DOI

10.1109/ICBBE.2009.5162487

Filename

5162487