Abstract
Mucin-type O-glycosylation is one of the main types of the mammalian protein glycosylation. It is serine (Ser) or threonine (Thr) specific, though any consensus sequence is still unknown. In this report, support vector machines (SVM) are used for the prediction of O-glycosylation for each Ser or Thr site in the protein sequences. 29 mammalian protein sequences are selected from UniProt8.0, and its structure information is obtained from Protein Data Bank (PDB). A protein subsequence with a prediction target of Ser or Thr site at the center is used as input to SVM, and its amino acid sequence information, and the secondary structure or accessibility, which are calculated by DSSP from PDB data, are encoded as an input data. The results of the preliminary experiments show the effectiveness of the local structure information added to the sequence information.
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References
Taylor, M.E., Drickamer, K.: Introduction to Glycobiology. Oxford Univ. Press, Oxford (2003)
Cristianini, N., S.-Taylor, J.: An Introduction to Support Vector Machines and other kernel-based learning methods. Cambridge University Press, Cambridge (2000)
Julenius, K., Molgaard, A., Gupta, R., Brunak, S.: Prediction, conservation analysis, and structural characterization of mammalian mucin-type O-glycosylation sites. Glycobiology 15(2), 153–164 (2004)
Li, S., Liu, B., Zeng, R., Cai, Y., Li, Y.: Predicting O-glycosylation sites in mammalian proteins by using SVMs. Computational Biology and Chemistry 30, 203–208 (2006)
Nishikawa, I., et al.: Prediction of the O-glycosylation sites in protein by layered neural networks and support vector machines. In: Gabrys, B., Howlett, R.J., Jain, L.C. (eds.) KES 2006. LNCS (LNAI), vol. 4252, pp. 953–960. Springer, Heidelberg (2006)
Nouno, I., et al.: Prediction of mucin-type O-glycosylation by layered neural networks and support vector machines. In: Proceedings of the 17th Int. Conference on Genome Informatics (December 2006)
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Nishikawa, I., Sakamoto, H., Nouno, I., Sakakibara, K., Ito, M. (2007). Prediction of the O-Glycosylation with Secondary Structure Information by Support Vector Machines. In: Apolloni, B., Howlett, R.J., Jain, L. (eds) Knowledge-Based Intelligent Information and Engineering Systems. KES 2007. Lecture Notes in Computer Science(), vol 4693. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-74827-4_43
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DOI: https://doi.org/10.1007/978-3-540-74827-4_43
Publisher Name: Springer, Berlin, Heidelberg
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