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Bioinformatics Vol. 17 no. 12 2001
Pages 1123-1130
© 2001 Oxford University Press

A probabilistic method for identifying start codons in bacterial genomes

Baris E. Suzek 1, Maria D. Ermolaeva 2, Mark Schreiber 3 and Steven L. Salzberg 1,2,*

1 Department of Computer Science, Johns Hopkins University, Baltimore, MD 21218, USA
2 The Institute for Genomic Research, 9712 Medical Center Dr, Rockville, MD 20850, USA
3 Department of Biochemistry, University of Otago, PO Box 56, Dunedin, New Zealand

Received on December 18, 2000 ; revised on July 4, 2001 ; accepted on July 9, 2001

As the pace of genome sequencing has accelerated, the need for highly accurate gene prediction systems has grown. Computational systems for identifying genes in prokaryotic genomes have sensitivities of 98–99% or higher (Delcher et al. , Nucleic Acids Res. , 27, 4636–4641, 1999). These accuracy figures are calculated by comparing the locations of verified stop codons to the predictions. Determining the accuracy of start codon prediction is more problematic, however, due to the relatively small number of start sites that have been confirmed by independent, non-computational methods. Nonetheless, the accuracy of gene finders at predicting the exact gene boundaries at both the 5' and 3' ends of genes is of critical importance for microbial genome annotation, especially in light of the important signaling information that is sometimes found on the 5' end of a protein coding region. In this paper we propose a probabilistic method to improve the accuracy of gene identification systems at finding precise translation start sites. The new system, RBSfinder, is tested on a validated set of genes from Escherichia coli , for which it improves the accuracy of start site locations predicted by computational gene finding systems from the range 67–77% to 90% correct.

* To whom correspondence should be addressed.


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