Least-Squares Support Vector Machine Approach to Viral Replication Origin Prediction

Authors:
Raul Cruz-Cano;David S. H. Chew;Kwok-Pui Choi;Ming-Ying Leung
Affiliations:
Department of Computer Science, Texas A&M University--Texarkana, Texarkana, Texas 75505;Department of Statistics and Applied Probability, National University of Singapore, Singapore 117546, Singapore, and Molecular and Computational Biology Program, Department of Biological Sciences, ...;Department of Statistics and Applied Probability, National University of Singapore, Singapore 117546, Singapore;Bioinformatics Program and Department of Mathematical Sciences, University of Texas at El Paso, El Paso, Texas 79968
Venue:
INFORMS Journal on Computing
Year:
2010

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Abstract

Replication of their DNA genomes is a central step in the reproduction of many viruses. Procedures to find replication origins, which are initiation sites of the DNA replication process, are therefore of great importance for controlling the growth and spread of such viruses. Existing computational methods for viral replication origin prediction have mostly been tested within the family of herpesviruses. This paper proposes a new approach by least-squares support vector machines (LS-SVMs) and tests its performance not only on the herpes family but also on a collection of caudoviruses coming from three viral families under the order of caudovirales. The LS-SVM approach provides sensitivities and positive predictive values superior or comparable to those given by the previous methods. When suitably combined with previous methods, the LS-SVM approach further improves the prediction accuracy for the herpesvirus replication origins. Furthermore, by recursive feature elimination, the LS-SVM has also helped find the most significant features of the data sets. The results suggest that the LS-SVMs will be a highly useful addition to the set of computational tools for viral replication origin prediction and illustrate the value of optimization-based computing techniques in biomedical applications.