Open Access Research Article

TRII: A Probabilistic Scoring of Drosophila melanogaster Translation Initiation Sites

Michael P Weir1* and Michael D Rice2

Author Affiliations

1 Department of Biology , Wesleyan University, Middletown, CT 06459, USA

2 Department of Mathematics and Computer Science, Wesleyan University , Middletown, CT 06459, USA

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EURASIP Journal on Bioinformatics and Systems Biology 2010, 2010:814127  doi:10.1155/2010/814127

Published: 18 October 2010

Abstract

Relative individual information is a measurement that scores the quality of DNA- and RNA-binding sites for biological machines. The development of analytical approaches to increase the power of this scoring method will improve its utility in evaluating the functions of motifs. In this study, the scoring method was applied to potential translation initiation sites in Drosophila to compute Translation Relative Individual Information (TRII) scores. The weight matrix at the core of the scoring method was optimized based on high-confidence translation initiation sites identified by using a progressive partitioning approach. Comparing the distributions of TRII scores for sites of interest with those for high-confidence translation initiation sites and random sequences provides a new methodology for assessing the quality of translation initiation sites. The optimized weight matrices can also be used to describe the consensus at translation initiation sites, providing a quantitative measure of preferred and avoided nucleotides at each position.