Accuracy improvement for identifying translation initiation sites in microbial genomes

Bioinformatics
Huaiqiu ZhuZhen-Su She

Abstract

At present the computational gene identification methods in microbial genomes have a high prediction accuracy of verified translation termination site (3' end), but a much lower accuracy of the translation initiation site (TIS, 5' end). The latter is important to the analysis and the understanding of the putative protein of a gene and the regulatory machinery of the translation. Improving the accuracy of prediction of TIS is one of the remaining open problems. In this paper, we develop a four-component statistical model to describe the TIS of prokaryotic genes. The model incorporates several features with biological meanings, including the correlation between translation termination site and TIS of genes, the sequence content around the start codon; the sequence content of the consensus signal related to ribosomal binding sites (RBSs), and the correlation between TIS and the upstream consensus signal. An entirely non-supervised training system is constructed, which takes as input a set of annotated coding open reading frames (ORFs) by any gene finder, and gives as output a set of organism-specific parameters (without any prior knowledge or empirical constants and formulas). The novel algorithm is tested on a set of reliable dat...Continue Reading

Citations

Jul 4, 2012·Journal of Biosciences·Garima KhandelwalB Jayaram
May 4, 2010·Nature Methods·Amrita PatiNikos C Kyrpides
Jan 24, 2007·Bioinformatics·Arthur L DelcherSteven L Salzberg
Nov 19, 2008·Bioinformatics·Gang-Qing HuZhen-Su She
Jun 14, 2013·BMC Bioinformatics·Yongchu LiuHuaiqiu Zhu
Mar 11, 2006·BMC Bioinformatics·Maike Tech, Peter Meinicke
Mar 28, 2008·BMC Bioinformatics·Gang-Qing HuZhen-Su She
Jun 21, 2007·PLoS Biology·Jian XuJeffrey I Gordon
Apr 26, 2008·PLoS Computational Biology·Liping Wei, Jun Yu
Oct 21, 2009·Journal of Theoretical Biology·Tingting GaoLing Jing
May 1, 2010·Microbiology·Maria S Poptsova, J Peter Gogarten

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