Computer Department, Jing-De-Zhen Ceramic Institute, Jing-De-Zhen 333046, China.
J Theor Biol. 2010 Nov 7;267(1):29-34. doi: 10.1016/j.jtbi.2010.08.007. Epub 2010 Aug 7.
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.
图形表示生物序列可以提供直观的整体图像，并为进行大规模分析提供有用的见解。这里提出了一种新的二维图形，称为“2D-MH”，用于表示蛋白质序列。它是通过合并组成氨基酸的每个侧链质量及其疏水性的信息而形成的。由此生成的图形曲线具有以下特点：(1) 一一对应关系，没有电路或退化；(2) 更好地反映蛋白质序列的固有结构；(3) 清晰地显示蛋白质序列的相似性；(4) 对药物靶向的重要突变位点更敏感；(5) 可用作蛋白质从一个物种到另一个物种的“进化距离”的度量。预计所提出的图形方法可能成为在后基因组时代产生的大量蛋白质序列进行大规模分析的有用工具。作为一个网络服务器，2D-MH 可在 http://icpr.jci.jx.cn/bioinfo/pplot/2D-MH 上免费访问，通过该服务器可以轻松生成任意数量的蛋白质序列的二维图形，并比较它们之间的进化距离。
