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Title: Prediction of Translation Initiation Sites Using Classifier Selection
Author(s): G. Tzanis, I. Vlahavas.
Availability: Click here to download the PDF (Acrobat Reader) file (11 pages).
Appeared in: Proc. 4th Hellenic Conference on Artificial Intelligence (SETN-06), G. Antoniou, G. Potamias, D. Plexousakis, C. Spyropoulos (Ed.), Springer-Verlag, LNAI 3955, pp. 367-377, Heraklion, Crete, 18-20 May, 2006.
Abstract: The prediction of the translation initiation site (TIS) in a genomic sequence is an important issue in biological research. Several methods have been proposed to deal with it. However, it is still an open problem. In this paper we follow an approach consisting of a number of steps in order to increase TIS prediction accuracy. First, all the sequences are scanned and the candidate TISs are detected. These sites are grouped according to the length of the sequence upstream and downstream them and a number of features is generated for each one. The features are evaluated among the instances of every group and a number of the top ranked ones are selected for building a classifier. A new instance is assigned to a group and is classified by the corresponding classifier. We experiment with various feature sets and classification algorithms, compare with alternative methods and draw important conclusions.
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1 Selpi, C. H. Bryant, G. J. L. Kemp, M. Cvijovic. A First Step towards Learning which uORFs Regulate Gene Expression. Journal of Integrative Bioinformatics, 3 (2 ), pp. 31-45, 2006.
2 C. N. Nobre, J. M. Ortega, A. de Padua Braga. High Efficiency on Prediction of Translation Initiation Site (TIS) of RefSeq Sequences. In Proceedings of the Second Brazilian Symposium on Bioinformatics (BSB 2007), Springer-Verlag, pp. 138-148, 2007
3 Jia Zeng, Alhajj, R., Demetrick, D., “Effectiveness of Applying Codon Usage Bias for Translational Initiation Sites Prediction”. In Proceedings of the IEEE International Conference of Bioinformatics and Biomedicine, 2008, pp.121-126, 2008.
4 S. Tikole, R. Sankararamakrishnan, Prediction of Translation Initiation Sites in Human mRNA Sequences with AUG Start Codon in Weak Kozak Context: A Neural Network Approach, Biochemical and Biophysical Research Communications. 369(4), pp. 1166-1168, 2008.