using support vector machine and evolutionary profiles to predict antifreeze protein sequences使用支持向量机和进化预测抗冻蛋白质序列.pdfVIP

Int. J. Mol. Sci. 2012, 13, 2196-2207; doi:10.3390/ijm OPEN ACCESS International Journal of Molecular Sciences ISSN 1422-0067 /journal/ijms Article Using Support Vector Machine and Evolutionary Profiles to Predict Antifreeze Protein Sequences Xiaowei Zhao 1,2,3, Zhiqiang Ma 1,2,3,* and Minghao Yin 1,2,* 1 College of Computer Science and Information Technology, Northeast Normal University, 2555 Jingyue Street, Changchun 130117, China; E-Mail: zhaoxw303@ 2 Key Laboratory of Intelligent Information Processing of Jilin Universities, Northeast Normal University, Changchun 130117, China 3 College of Life Science, Northeast Normal University, 5268 Renmin Street, Changchun 130024, China * Authors to whom correspondence should be addressed; E-Mails: zhiqiang.ma967@ (Z.M.); minghao.yin197@ (M.Y.); Tel./Fax: +86-0431-8453-6338 (Z.M.; M.Y.). Received: 5 January 2012; in revised form: 29 January 2012 / Accepted: 29 January 2012 / Published: 17 February 2012 Abstract: Antifreeze proteins (AFPs) are ice-binding proteins. Accurate identification of new AFPs is important in understanding ice-protein interactions and creating novel ice-binding domains in other proteins. In this paper, an accurate method, called AFP_PSSM, has been developed for predicting antifreeze proteins using a support vector machine (SVM) and position specific scoring matrix (PSSM) profiles. This is the first study in which evolutionary information in