Abstract
Protein and peptide sequences contain clues for functional prediction. A challenge is to predict sequences that show low or no homology to proteins or peptides of known function. A machine learning method, support vector machines (SVM), has recently been explored for predicting functional class of proteins and peptides from sequence-derived properties irrespective of sequence similarity, which has shown impressive performance for predicting a wide range of protein and peptide classes including certain low- and non- homologous sequences. This method serves as a new and valuable addition to complement the extensively-used alignment-based, clustering-based, and structure-based functional prediction methods. This article evaluates the strategies, current progresses, reported prediction performances, available software tools, and underlying difficulties in using SVM for predicting the functional class of proteins and peptides.
Keywords: Machine learning method, peptide, peptide function, protein family, protein function, protein function prediction, protein sequence, support vector machine
Current Protein & Peptide Science
Title: Homology-Free Prediction of Functional Class of Proteins and Peptides by Support Vector Machines
Volume: 9 Issue: 1
Author(s): Y. Z. Chen, F. Zhu, L. Y. Han, X. Chen, H. H. Lin, S. Ong, B. Xie and H. L. Zhang
Affiliation:
Keywords: Machine learning method, peptide, peptide function, protein family, protein function, protein function prediction, protein sequence, support vector machine
Abstract: Protein and peptide sequences contain clues for functional prediction. A challenge is to predict sequences that show low or no homology to proteins or peptides of known function. A machine learning method, support vector machines (SVM), has recently been explored for predicting functional class of proteins and peptides from sequence-derived properties irrespective of sequence similarity, which has shown impressive performance for predicting a wide range of protein and peptide classes including certain low- and non- homologous sequences. This method serves as a new and valuable addition to complement the extensively-used alignment-based, clustering-based, and structure-based functional prediction methods. This article evaluates the strategies, current progresses, reported prediction performances, available software tools, and underlying difficulties in using SVM for predicting the functional class of proteins and peptides.
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Cite this article as:
Chen Z. Y., Zhu F., Han Y. L., Chen X., Lin H. H., Ong S., Xie B. and Zhang L. H., Homology-Free Prediction of Functional Class of Proteins and Peptides by Support Vector Machines, Current Protein & Peptide Science 2008; 9 (1) . https://dx.doi.org/10.2174/138920308783565697
DOI https://dx.doi.org/10.2174/138920308783565697 |
Print ISSN 1389-2037 |
Publisher Name Bentham Science Publisher |
Online ISSN 1875-5550 |
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