Journal Article

LOCSVMPSI: a web server for subcellular localization of eukaryotic proteins using SVM and profile of PSI-BLAST

Dan Xie, Ao Li, Minghui Wang, Zhewen Fan and Huanqing Feng

in Nucleic Acids Research

Volume 33, issue suppl_2, pages W105-W110
Published in print July 2005 | ISSN: 0305-1048
Published online July 2005 | e-ISSN: 1362-4962 | DOI: http://dx.doi.org/10.1093/nar/gki359

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Subcellular location of a protein is one of the key functional characters as proteins must be localized correctly at the subcellular level to have normal biological function. In this paper, a novel method named LOCSVMPSI has been introduced, which is based on the support vector machine (SVM) and the position-specific scoring matrix generated from profiles of PSI-BLAST. With a jackknife test on the RH2427 data set, LOCSVMPSI achieved a high overall prediction accuracy of 90.2%, which is higher than the prediction results by SubLoc and ESLpred on this data set. In addition, prediction performance of LOCSVMPSI was evaluated with 5-fold cross validation test on the PK7579 data set and the prediction results were consistently better than the previous method based on several SVMs using composition of both amino acids and amino acid pairs. Further test on the SWISSPROT new-unique data set showed that LOCSVMPSI also performed better than some widely used prediction methods, such as PSORTII, TargetP and LOCnet. All these results indicate that LOCSVMPSI is a powerful tool for the prediction of eukaryotic protein subcellular localization. An online web server (current version is 1.3) based on this method has been developed and is freely available to both academic and commercial users, which can be accessed by at http://Bioinformatics.ustc.edu.cn/LOCSVMPSI/LOCSVMPSI.php.

Journal Article.  3228 words.  Illustrated.

Subjects: Chemistry ; Biochemistry ; Bioinformatics and Computational Biology ; Genetics and Genomics ; Molecular and Cell Biology

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