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Bacillus Genetic Stock Center, Department of Biochemistry, The Ohio State University, Columbus, OH 43210, USA
Correspondence
Daniel R. Zeigler
zeigler.1{at}osu.edu
Thirty-two protein-encoding genes that are distributed widely among bacterial genomes were tested for the potential usefulness of their DNA sequences in assigning bacterial strains to species. From publicly available data, it was possible to make 49 pairwise comparisons of whole bacterial genomes that were related at the genus or subgenus level. DNA sequence identity scores for eight of the genes correlated strongly with overall sequence identity scores for the genome pairs. Even single-gene alignments could predict overall genome relatedness with a high degree of precision and accuracy. Predictions could be refined further by including two or three genes in the analysis. The proposal that sequence analysis of a small set of protein-encoding genes could reliably assign novel strains or isolates to bacterial species is strongly supported.
A spreadsheet listing sequence identity scores for all candidates with each genome comparison is available as supplementary data in IJSEM Online.
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|
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|
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|
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|
|
|
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|
|
|
|
|
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|
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|
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|
|
|
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