Molecular Biology and Evolution, Vol 16, 512-524, Copyright © 1999 by Society for Molecular Biology and Evolution
JH Badger and GJ Olsen
Gene recognition is essential to understanding existing and future DNA
sequence data. CRITICA (Coding Region Identification Tool Invoking
Comparative Analysis) is a suite of programs for identifying likely
protein-coding sequences in DNA by combining comparative analysis of DNA
sequences with more common noncomparative methods. In the comparative
component of the analysis, regions of DNA are aligned with related
sequences from the DNA databases; if the translation of the aligned
sequences has greater amino acid identity than expected for the observed
percentage nucleotide identity, this is interpreted as evidence for coding.
CRITICA also incorporates noncomparative information derived from the
relative frequencies of hexanucleotides in coding frames versus other
contexts (i.e., dicodon bias). The dicodon usage information is derived by
iterative analysis of the data, such that CRITICA is not dependent on the
existence or accuracy of coding sequence annotations in the databases. This
independence makes the method particularly well suited for the analysis of
novel genomes. CRITICA was tested by analyzing the available Salmonella
typhimurium DNA sequences. Its predictions were compared with the DNA
sequence annotations and with the predictions of GenMark. CRITICA proved to
be more accurate than GenMark, and moreover, many of its predictions that
would seem to be errors instead reflect problems in the sequence databases.
The source code of CRITICA is freely available by anonymous FTP
(rdp.life.uiuc.edu in/pub/critica) and on the World Wide Web
(http:/(/)rdpwww.life.uiuc.edu).
ORIGINAL ARTICLE
CRITICA: coding region identification tool invoking comparative analysis
Department of Microbiology, University of Illinois, Urbana 61801, USA.
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