期刊
JOURNAL OF THEORETICAL BIOLOGY
卷 267, 期 1, 页码 29-34出版社
ACADEMIC PRESS LTD- ELSEVIER SCIENCE LTD
DOI: 10.1016/j.jtbi.2010.08.007
关键词
Sequence visualization; Side-chain mass; Hydrophobicity; Main eigenvalues; Evolutionary vector
资金
- National Natural Science Foundation of China [60961003]
- Key Project of Chinese Ministry of Education [210116]
- Province National Natural Science Foundation of JiangXi [2009GZS0064]
- Department of Education of JiangXi Province [GJJ09271]
- plan for training youth scientists (stars of Jing-Gang) of Jiangxi Province
Introduction of graphic representation for biological sequences can provide intuitive overall pictures as well as useful insights for performing large-scale analysis. Here, a new two-dimensional graph, called 2D-MH, is proposed to represent protein sequences. It is formed by incorporating the information of the side-chain mass of each of the constituent amino acids and its hydrophobicity. The graphic curve thus generated is featured by (1) an one-to-one correspondence relation without circuit or degeneracy, (2) better reflecting the innate structure of the protein sequence, (3) clear visibility in displaying the similarity of protein sequences, (4) more sensitive for the mutation sites important for drug targeting, and (5) being able to be used as a metric for the evolutionary distance of a protein from one species to the other. It is anticipated that the presented graphic method may become a useful vehicle for large-scale analysis of the avalanche of protein sequences generated in the post-genomic age. As a web-server, 2D-MH is freely accessible at http://icpr.jci.jx.cn/bioinfo/pplot/2D-MH, by which one can easily generate the two-dimensional graphs for any number of protein sequences and compare the evolutionary distances between them. (C) 2010 Elsevier Ltd. All rights reserved.
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