Support vector machine prediction of N-and O-glycosylation sites using whole sequence information and subcellular localization

Kenta Sasaki, Nobuyoshi Nagamine, Yasubumi Sakakibara

Research output: Contribution to journalArticlepeer-review

18 Citations (Scopus)

Abstract

Background: Glycans, or sugar chains, are one of the three types of chain (DNA, protein and glycan) that constitute living organisms; they are often called "the third chain of the living organism". About half of all proteins are estimated to be glycosylated based on the SWISS-PROT database. Glycosylation is one of the most important post-translational modifications, affecting many critical functions of proteins, including cellular communication, and their tertiary structure. In order to computationally predict N-glycosylation and O-glycosylation sites, we developed three kinds of support vector machine (SVM) model, which utilize local information, general protein information and/or subcellular localization in consideration of the binding specificity of glycosyltransferases and the characteristic subcellular localization of glycoproteins. Results: In our computational experiment, the model integrating three kinds of information achieved about 90% accuracy in predictions of both N-glycosylation and O-glycosylation sites. Moreover, our model was applied to a protein whose glycosylation sites had not been previously identified and we succeeded in showing that the glycosylation sites predicted by our model were structurally reasonable. Conclusions: In the present study, we developed a comprehensive and effective computational method that detects glycosylation sites. We conclude that our method is a comprehensive and effective computational prediction method that is applicable at a genome-wide level.

Original languageEnglish
Pages (from-to)25-35
Number of pages11
JournalIPSJ Transactions on Bioinformatics
Volume2
DOIs
Publication statusPublished - 2009

ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology (miscellaneous)
  • Computer Science Applications

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