Journal Article

A Novel Bacterial Gene-Finding System with Improved Accuracy in Locating Start Codons

Tetsushi Yada, Yasushi Totoki, Toshihisa Takagi and Kenta Nakai

in DNA Research

Published on behalf of Kazusa DNA Research Institute

Volume 8, issue 3, pages 97-106
Published in print January 2001 | ISSN: 1340-2838
Published online January 2001 | e-ISSN: 1756-1663 | DOI: http://dx.doi.org/10.1093/dnares/8.3.97

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Although a number of bacterial gene finding programs have been developed, there is still room for improvement especially in the area of correctly detecting translation start sites. We developed a novel bacterial gene finding program named GeneHacker Plus. Like many others, it is based on a hidden Markov model (HMM) with duration. However, it is a ‘local’ model in the sense that the model starts from the translation control region and ends at the stop codon of a coding region. Multiple coding regions are identi.ed as partial paths, like local alignments in the Smith-Waterman algorithm, regardless of how they overlap. Moreover, our semiautomatic procedure for constructing the model of the translation control region allows the inclusion of an additional conserved element as well as the ribosome-binding site. We confirmed that GeneHacker Plus is one of the most accurate programs in terms of both finding potential coding regions and precisely locating translation start sites. GeneHacker Plus is also equipped with an option where the results from database homology searches are directly embedded in the HMM. Although this option does not raise the overall predictability, labeled similarity information can be of practical use. GeneHacker Plus can be accessed freely at .

Keywords: gene finding; hidden Markov model; start codon; genome analysis; ribosome binding site

Journal Article.  0 words. 

Subjects: Genetics and Genomics

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