PMID:9611239
| Citation |
Frishman, D, Mironov, A, Mewes, HW and Gelfand, M (1998) Combining diverse evidence for gene recognition in completely sequenced bacterial genomes. Nucleic Acids Res. 26:2941-7 |
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| 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. |
| Links | |
| Keywords |
Algorithms; Bacillus subtilis/genetics; Bacterial Proteins/genetics; Codon, Initiator; Databases, Factual; Escherichia coli/genetics; Genome, Bacterial; Open Reading Frames; Sequence Alignment/methods; Sequence Analysis, DNA; Software |
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