Engineering support vector machine kernels that recognize translation initiation sites
Alexander Zien,Gunnar Rätsch,Sebastian Mika,Bernhard Schölkopf,Thomas Lengauer,Klaus-Robert Müller +5 more
- 01 Sep 2000
- Vol. 16, Iss: 9, pp 799-807
477
TL;DR: Zien et al. as discussed by the authors used support vector machines (SVM) to identify the translation initiation sites (TIS) in protein sequences from nucleotide sequences, which is an important step to recognize points at which regions start that code for proteins.
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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. Contact: {Alexander.Zien,Gunnar.Raetsch,Sebastian.
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