The theoretical basis of universal identification systems for bacteria and viruses.
Identifieur interne : 002297 ( PubMed/Corpus ); précédent : 002296; suivant : 002298The theoretical basis of universal identification systems for bacteria and viruses.
Auteurs : S. Chumakov ; C. Belapurkar ; C. Putonti ; T-B Li ; B M Pettitt ; G E Fox ; R C Willson ; Yu FofanovSource :
- Journal of biological physics and chemistry : JBPC [ 1512-0856 ] ; 2005.
Abstract
It is shown that the presence/absence pattern of 1000 random oligomers of length 12-13 in a bacterial genome is sufficiently characteristic to readily and unambiguously distinguish any known bacterial genome from any other. Even genomes of extremely closely-related organisms, such as strains of the same species, can be thus distinguished. One evident way to implement this approach in a practical assay is with hybridization arrays. It is envisioned that a single universal array can be readily designed that would allow identification of any bacterium that appears in a database of known patterns. We performed in silico experiments to test this idea. Calculations utilizing 105 publicly-available completely-sequenced microbial genomes allowed us to determine appropriate values of the test oligonucleotide length, n, and the number of probe sequences. Randomly chosen n-mers with a constant G + C content were used to form an in silico array and verify (a) how many n-mers from each genome would hybridize on this chip, and (b) how different the fingerprints of different genomes would be. With the appropriate choice of random oligomer length, the same approach can also be used to identify viral or eukaryotic genomes.
DOI: 10.4024/40501.jbpc.05.04
PubMed: 20428334
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pubmed:20428334Le document en format XML
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<front><div type="abstract" xml:lang="en">It is shown that the presence/absence pattern of 1000 random oligomers of length 12-13 in a bacterial genome is sufficiently characteristic to readily and unambiguously distinguish any known bacterial genome from any other. Even genomes of extremely closely-related organisms, such as strains of the same species, can be thus distinguished. One evident way to implement this approach in a practical assay is with hybridization arrays. It is envisioned that a single universal array can be readily designed that would allow identification of any bacterium that appears in a database of known patterns. We performed in silico experiments to test this idea. Calculations utilizing 105 publicly-available completely-sequenced microbial genomes allowed us to determine appropriate values of the test oligonucleotide length, n, and the number of probe sequences. Randomly chosen n-mers with a constant G + C content were used to form an in silico array and verify (a) how many n-mers from each genome would hybridize on this chip, and (b) how different the fingerprints of different genomes would be. With the appropriate choice of random oligomer length, the same approach can also be used to identify viral or eukaryotic genomes.</div>
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<Abstract><AbstractText>It is shown that the presence/absence pattern of 1000 random oligomers of length 12-13 in a bacterial genome is sufficiently characteristic to readily and unambiguously distinguish any known bacterial genome from any other. Even genomes of extremely closely-related organisms, such as strains of the same species, can be thus distinguished. One evident way to implement this approach in a practical assay is with hybridization arrays. It is envisioned that a single universal array can be readily designed that would allow identification of any bacterium that appears in a database of known patterns. We performed in silico experiments to test this idea. Calculations utilizing 105 publicly-available completely-sequenced microbial genomes allowed us to determine appropriate values of the test oligonucleotide length, n, and the number of probe sequences. Randomly chosen n-mers with a constant G + C content were used to form an in silico array and verify (a) how many n-mers from each genome would hybridize on this chip, and (b) how different the fingerprints of different genomes would be. With the appropriate choice of random oligomer length, the same approach can also be used to identify viral or eukaryotic genomes.</AbstractText>
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<ReferenceList><Reference><Citation>Syst Appl Microbiol. 2003 Jun;26(2):262-8</Citation>
<ArticleIdList><ArticleId IdType="pubmed">12866853</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>Genome Res. 1998 May;8(5):435-48</Citation>
<ArticleIdList><ArticleId IdType="pubmed">9582189</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>J Clin Periodontol. 1991 Jul;18(6):396-405</Citation>
<ArticleIdList><ArticleId IdType="pubmed">1890219</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>Appl Environ Microbiol. 2003 Aug;69(8):4942-50</Citation>
<ArticleIdList><ArticleId IdType="pubmed">12902290</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>Appl Environ Microbiol. 2002 Nov;68(11):5452-8</Citation>
<ArticleIdList><ArticleId IdType="pubmed">12406737</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>Nucleic Acids Res. 2003 Jan 15;31(2):779-89</Citation>
<ArticleIdList><ArticleId IdType="pubmed">12527788</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>Appl Environ Microbiol. 2002 Dec;68(12):6361-70</Citation>
<ArticleIdList><ArticleId IdType="pubmed">12450861</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>Nucleic Acids Res. 2004 Mar 22;32(5):1848-56</Citation>
<ArticleIdList><ArticleId IdType="pubmed">15037662</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>Bioinformatics. 2004 Oct 12;20(15):2421-8</Citation>
<ArticleIdList><ArticleId IdType="pubmed">15087315</ArticleId>
</ArticleIdList>
</Reference>
</ReferenceList>
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