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Comprehensive DNA Signature Discovery and Validation

DNA signatures are nucleotide sequences that can be used to detect the presence of an organism and to distinguish that organism from all other species. Here we describe Insignia, a new, comprehensive system for the rapid identification of signatures in the genomes of bacteria and viruses. With the a...

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Autores principales: Phillippy, Adam M, Mason, Jacquline A, Ayanbule, Kunmi, Sommer, Daniel D, Taviani, Elisa, Huq, Anwar, Colwell, Rita R, Knight, Ivor T, Salzberg, Steven L
Formato: Texto
Lenguaje:English
Publicado: Public Library of Science 2007
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1868776/
https://www.ncbi.nlm.nih.gov/pubmed/17511514
http://dx.doi.org/10.1371/journal.pcbi.0030098
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author Phillippy, Adam M
Mason, Jacquline A
Ayanbule, Kunmi
Sommer, Daniel D
Taviani, Elisa
Huq, Anwar
Colwell, Rita R
Knight, Ivor T
Salzberg, Steven L
author_facet Phillippy, Adam M
Mason, Jacquline A
Ayanbule, Kunmi
Sommer, Daniel D
Taviani, Elisa
Huq, Anwar
Colwell, Rita R
Knight, Ivor T
Salzberg, Steven L
author_sort Phillippy, Adam M
collection PubMed
description DNA signatures are nucleotide sequences that can be used to detect the presence of an organism and to distinguish that organism from all other species. Here we describe Insignia, a new, comprehensive system for the rapid identification of signatures in the genomes of bacteria and viruses. With the availability of hundreds of complete bacterial and viral genome sequences, it is now possible to use computational methods to identify signature sequences in all of these species, and to use these signatures as the basis for diagnostic assays to detect and genotype microbes in both environmental and clinical samples. The success of such assays critically depends on the methods used to identify signatures that properly differentiate between the target genomes and the sample background. We have used Insignia to compute accurate signatures for most bacterial genomes and made them available through our Web site. A sample of these signatures has been successfully tested on a set of 46 Vibrio cholerae strains, and the results indicate that the signatures are highly sensitive for detection as well as specific for discrimination between these strains and their near relatives. Our approach, whereby the entire genomic complement of organisms are compared to identify probe targets, is a promising method for diagnostic assay development, and it provides assay designers with the flexibility to choose probes from the most relevant genes or genomic regions. The Insignia system is freely accessible via a Web interface and has been released as open source software at: http://insignia.cbcb.umd.edu.
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spelling pubmed-18687762007-05-18 Comprehensive DNA Signature Discovery and Validation Phillippy, Adam M Mason, Jacquline A Ayanbule, Kunmi Sommer, Daniel D Taviani, Elisa Huq, Anwar Colwell, Rita R Knight, Ivor T Salzberg, Steven L PLoS Comput Biol Research Article DNA signatures are nucleotide sequences that can be used to detect the presence of an organism and to distinguish that organism from all other species. Here we describe Insignia, a new, comprehensive system for the rapid identification of signatures in the genomes of bacteria and viruses. With the availability of hundreds of complete bacterial and viral genome sequences, it is now possible to use computational methods to identify signature sequences in all of these species, and to use these signatures as the basis for diagnostic assays to detect and genotype microbes in both environmental and clinical samples. The success of such assays critically depends on the methods used to identify signatures that properly differentiate between the target genomes and the sample background. We have used Insignia to compute accurate signatures for most bacterial genomes and made them available through our Web site. A sample of these signatures has been successfully tested on a set of 46 Vibrio cholerae strains, and the results indicate that the signatures are highly sensitive for detection as well as specific for discrimination between these strains and their near relatives. Our approach, whereby the entire genomic complement of organisms are compared to identify probe targets, is a promising method for diagnostic assay development, and it provides assay designers with the flexibility to choose probes from the most relevant genes or genomic regions. The Insignia system is freely accessible via a Web interface and has been released as open source software at: http://insignia.cbcb.umd.edu. Public Library of Science 2007-05 2007-05-18 /pmc/articles/PMC1868776/ /pubmed/17511514 http://dx.doi.org/10.1371/journal.pcbi.0030098 Text en © 2007 Phillippy et al. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.
spellingShingle Research Article
Phillippy, Adam M
Mason, Jacquline A
Ayanbule, Kunmi
Sommer, Daniel D
Taviani, Elisa
Huq, Anwar
Colwell, Rita R
Knight, Ivor T
Salzberg, Steven L
Comprehensive DNA Signature Discovery and Validation
title Comprehensive DNA Signature Discovery and Validation
title_full Comprehensive DNA Signature Discovery and Validation
title_fullStr Comprehensive DNA Signature Discovery and Validation
title_full_unstemmed Comprehensive DNA Signature Discovery and Validation
title_short Comprehensive DNA Signature Discovery and Validation
title_sort comprehensive dna signature discovery and validation
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1868776/
https://www.ncbi.nlm.nih.gov/pubmed/17511514
http://dx.doi.org/10.1371/journal.pcbi.0030098
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