Engineering support vector machine kernels that recognize translation initiation sites

A. Zien, G. Rätsch, S. Mika, B. Schölkopf, T. Lengauer, K. R. Müller

Research output: Contribution to journalArticle

296 Citations (Scopus)

Abstract

Motivation: In order to extract protein sequences from nucleotide sequences, it is an important step to recognize points at which regions start that code for proteins. These points are called translation initiation sites (TIS). Results: The task of finding TIS can be modeled as a classification problem. We demonstrate the applicability of support vector machines for this task, and show how to incorporate prior biological knowledge by engineering an appropriate kernel function. With the described techniques the recognition performance can be improved by 26% over leading existing approaches. We provide evidence that existing related methods (e.g. ESTScan) could profit from advanced TIS recognition.

Original languageEnglish
Pages (from-to)799-807
Number of pages9
JournalBioinformatics
Volume16
Issue number9
DOIs
Publication statusPublished - 2000
Externally publishedYes

ASJC Scopus subject areas

  • Statistics and Probability
  • Biochemistry
  • Molecular Biology
  • Computer Science Applications
  • Computational Theory and Mathematics
  • Computational Mathematics

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  • Cite this

    Zien, A., Rätsch, G., Mika, S., Schölkopf, B., Lengauer, T., & Müller, K. R. (2000). Engineering support vector machine kernels that recognize translation initiation sites. Bioinformatics, 16(9), 799-807. https://doi.org/10.1093/bioinformatics/16.9.799