Combining diverse evidence for gene recognition in completely sequenced bacterial genomes

Dmitrij Frishman, Andrey Mironov, Hans Werner Mewes, Mikhail Gelfand

Publikation: Beitrag in FachzeitschriftArtikelBegutachtung

151 Zitate (Scopus)

Abstract

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.

OriginalspracheEnglisch
Seiten (von - bis)2941-2947
Seitenumfang7
FachzeitschriftNucleic Acids Research
Jahrgang26
Ausgabenummer12
DOIs
PublikationsstatusVeröffentlicht - 15 Juni 1998
Extern publiziertJa

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