Prediction of protein subcellular localizations using moment descriptors and support vector machine

Authors:
Jianyu Shi;Shaowu Zhang;Yan Liang;Quan Pan
Affiliations:
College of Automation, Northwestern Polytechnical University, Xi'an, China;College of Automation, Northwestern Polytechnical University, Xi'an, China;College of Automation, Northwestern Polytechnical University, Xi'an, China;College of Automation, Northwestern Polytechnical University, Xi'an, China
Venue:
PRIB'06 Proceedings of the 2006 international conference on Pattern Recognition in Bioinformatics
Year:
2006

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Abstract

As more and more genomes have been discovered in recent years, it is an urgent need to develop a reliable method to predict protein subcellular localization for further function exploration. However many well-known prediction methods based on amino acid composition, have no ability to utilize the information of sequence-order. Here we propose a novel method, named moment descriptor (MD), which can obtain sequence order information in protein sequence without the need of the information of physicochemical properties of amino acids. The presented method first constructs three types of moment descriptors, and then applies multi-class SVM to the Chou's dataset. Through resubstitution, jackknife and independent tests, it is shown that the MD is better than other methods based on various types of extensions of amino acid compositions. Moreover, three multi-class SVMs show similar performance except for the training time.