Combining diverse evidence for gene recognition in completely sequenced bacterial genomes.
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.
Frishman
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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
Mironov
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A
Mewes
H W
HW
Gelfand
M
M
D000465:Algorithms; D001412:Bacillus subtilis / Q000235:genetics; D001426:Bacterial Proteins / Q000235:genetics; D018387:Codon, Initiator; D016208:Databases, Factual; D004926:Escherichia coli / Q000235:genetics; D016680:Genome, Bacterial; D016366:Open Reading Frames; D016415:Sequence Alignment / Q000379:methods*; D017422:Sequence Analysis, DNA; D012984:Software
D001426:Bacterial Proteins; D018387:Codon, Initiator