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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| Main Authors: | , , , , , , , , |
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| Format: | Article |
| Language: | English |
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Public Library of Science (PLoS)
2007-05-01
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| Series: | PLoS Computational Biology |
| Online Access: | https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.0030098&type=printable |
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| _version_ | 1850234011318747136 |
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| author | Adam M Phillippy Jacquline A Mason Kunmi Ayanbule Daniel D Sommer Elisa Taviani Anwar Huq Rita R Colwell Ivor T Knight Steven L Salzberg |
| author_facet | Adam M Phillippy Jacquline A Mason Kunmi Ayanbule Daniel D Sommer Elisa Taviani Anwar Huq Rita R Colwell Ivor T Knight Steven L Salzberg |
| author_sort | Adam M Phillippy |
| collection | DOAJ |
| 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. |
| format | Article |
| id | doaj-art-cd9b7c753bfe42e89d9d393e93aae490 |
| institution | OA Journals |
| issn | 1553-734X 1553-7358 |
| language | English |
| publishDate | 2007-05-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS Computational Biology |
| spelling | doaj-art-cd9b7c753bfe42e89d9d393e93aae4902025-08-20T02:02:44ZengPublic Library of Science (PLoS)PLoS Computational Biology1553-734X1553-73582007-05-0135e9810.1371/journal.pcbi.0030098Comprehensive DNA signature discovery and validation.Adam M PhillippyJacquline A MasonKunmi AyanbuleDaniel D SommerElisa TavianiAnwar HuqRita R ColwellIvor T KnightSteven L SalzbergDNA 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.https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.0030098&type=printable |
| spellingShingle | Adam M Phillippy Jacquline A Mason Kunmi Ayanbule Daniel D Sommer Elisa Taviani Anwar Huq Rita R Colwell Ivor T Knight Steven L Salzberg Comprehensive DNA signature discovery and validation. PLoS Computational Biology |
| 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 |
| url | https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.0030098&type=printable |
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