Classifying Genes Encode Transmembrane Proteins Using Neighboring Genes

Received: 06-10-2014

Accepted: 20-12-2014

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Issue: Vol. 13 No. 2 (2015)

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KỸ THUẬT VÀ CÔNG NGHỆ

How to Cite:

Ha, T., Dung, P., Thao, N., & Ha, D. (2024). Classifying Genes Encode Transmembrane Proteins Using Neighboring Genes. Vietnam Journal of Agricultural Sciences, 13(2), 291–300. http://testtapchi.vnua.edu.vn/index.php/vjasvn/article/view/163

Classifying Genes Encode Transmembrane Proteins Using Neighboring Genes

Tran Vu Ha (*) 1 , Pham Quang Dung 1 , Nguyen Thi Thao 1 , Doan Thi Thu Ha 1

  • 1 Khoa Công nghệ thông tin, Học viện Nông nghiệp Việt Nam

    • Keywords

    Gene Ontology, neighboring genes, transmembrane protein

    Abstract


    Like bio-diversity, there are too many proteins to experimentally annotate. Thus, methods for predicting the functions of proteins become necessary. In this article, we proposed a method that uses biological data to classify membrane transporters according to transported substrates. Motivated by the concept of Operons, our method used expression data and GO terms of neighboring genes to create input data for support vector machine. To rapidly obtain the result, we integrated LIBSVM in our tool then used this tool to train and test our classifiers. With this tool, users can classify membrane transporters and other kinds of proteins. This tool also allows users to add their desired organisms beside our tested ones.

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