Engineering Support Vector Machine Kernels That Recognize Translation Initiation Sites

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Engineering Support Vector Machine Kernels That Recognize Translation Initiation Sites (2000)

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

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133 - 14 self

BibTeX

@MISC{Zien00engineeringsupport,
    author = {A. Zien and G. Rätsch and S. Mika and B. Schölkopf and T. Lengauer and K.-R. Müller},
    title = {Engineering Support Vector Machine Kernels That Recognize Translation Initiation Sites},
    year = {2000}
}

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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 (SVMs) 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.

Keyphrases

recognize translation initiation site support vector machine kernel support vector machine appropriate kernel function recognition performance advanced ti recognition nucleotide sequence classification problem translation initiation site important step protein sequence prior biological knowledge

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