A Discriminative Framework for Detecting Remote Protein Homologies
Publication: Journal of Computational Biology
Volume 7, Issue Number 1-2
Abstract
A new method for detecting remote protein homologies is introduced and shown to perform well in classifying protein domains by SCOP superfamily. The method is a variant of support vector machines using a new kernel function. The kernel function is derived from a generative statistical model for a protein family, in this case a hidden Markov model. This general approach of combining generative models like HMMs with discriminative methods such as support vector machines may have applications in other areas of biosequence analysis as well.
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Published In
Journal of Computational Biology
Volume 7 • Issue Number 1-2 • February 2000
Pages: 95 - 114
PubMed: 10890390
History
Published online: 5 July 2004
Published in print: February 2000
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