Nucleic Acids Research, Vol 26, Issue 12 2941-2947, Copyright © 1998 by Oxford University Press
D Frishman, A Mironov, HW Mewes and M Gelfand
Analysis of a newly sequenced bacterial genome starts with identification
of protein-coding genes. Functional assignment of proteins requires the
exact knowledge of protein N-termini. We present a new program ORPHEUS that
identifies candidate genes and accurately predicts gene starts. The
analysis starts with a database similarity search and identification of
reliable gene fragments. The latter are used to derive statistical
characteristics of protein-coding regions and ribosome-binding sites and to
predict the complete set of genes in the analyzed genome. In a test on
Bacillus subtilis and Escherichia coli genomes, the program correctly
identified 93.3% (resp. 96.3%) of experimentally annotated genes longer
than 100 codons described in the PIR-International database, and for these
genes 96.3% (83.9%) of starts were predicted exactly. Furthermore, 98.9%
(99.1%) of genes longer than 100 codons annotated in GenBank were found,
and 92.9% (75.7%) of predicted starts coincided with the feature table
description. Finally, for the complete gene complements of B.subtilis and
E.coli , including genes shorter than 100 codons, gene prediction accuracy
was 88.9 and 87.1%, respectively, with 94.2 and 76.7% starts coinciding
with the existing annotation.
ARTICLES
Combining diverse evidence for gene recognition in completely sequenced bacterial genomes [published erratum appears in Nucleic Acids Res 1998 Aug 15;26(16):following 3870]
Munich Information Center for Protein Sequences (MIPS) of the German National Center for Health and Environment (GSF), Am Klopferspitz 18a, 82152 Martinsried, Germany. frishman@mips.biochem.mpg.de
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