Gene-finding with the VOM model

Article type: Research Article

Authors: Shohat-Zaidenraise, K.O.^b | Shmilovici, A.^{a; *} | Ben-Gal, I.^b

Affiliations: [a] Department of Information Systems Engineering, Ben-Gurion University, P.O. Box 653, Beer-Sheva 84105, Israel | [b] Department of Industrial Engineering, Tel-Aviv University, Ramat-Aviv, Tel-Aviv 69978, Israel

Correspondence: [*] Corresponding author. E-mail: [email protected].

Abstract: We present the architecture of an elementary gene-finding algorithm that is based on a Variable Order Markov model (VOM). The VOM model is a generalization of the traditional Markov model that can cope with varying memory dependencies. The VOM model is more efficient in terms of its parameterization and therefore can be trained on relatively short sequences. Experiments with the proposed gene-finder (GF) on three prokaryotic genomes indicate its potential advantage on the detection of short genes.

Keywords: Gene finding, Variable Order Markov models, sequence analysis

DOI: 10.3233/JCM-2007-7103

Journal: Journal of Computational Methods in Sciences and Engineering, vol. 7, no. 1, pp. 45-54, 2007