Non-standard similarity/dissimilarity analysis of DNA sequences
Similarity/dissimilarity analysis of DNA sequences is performed using 3D-dynamic representation. The sequences are represented by material points in a 3D-space. Descriptors related to such 3D-dynamic graphs are calculated. A new normalized similarity measure is introduced for a comparison of the seq...
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| Veröffentlicht in: | Genomics (San Diego, Calif.) Calif.), 2014-12, Vol.104 (6), p.464-471 |
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| container_title | Genomics (San Diego, Calif.) |
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| creator | Wąż, Piotr Bielińska-Wąż, Dorota |
| description | Similarity/dissimilarity analysis of DNA sequences is performed using 3D-dynamic representation. The sequences are represented by material points in a 3D-space. Descriptors related to such 3D-dynamic graphs are calculated. A new normalized similarity measure is introduced for a comparison of the sequences. The method is applied to β-globin (HBB) genes of different species. Different methods are compared. The multidimensionality of similarity space of complex objects is discussed (different results for each of the methods). It is also shown that it is easier to find the properties which are consistent with the observation of the evolution of the species for the second exons of β-globin gene rather than for the first ones.
•A new normalized similarity measure is introduced.•3D-dynamic representation of DNA sequences is applied for similarity analysis.•Multidimensionality of the similarity space of DNA sequences is discussed. |
| doi_str_mv | 10.1016/j.ygeno.2014.08.010 |
| format | Article |
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•A new normalized similarity measure is introduced.•3D-dynamic representation of DNA sequences is applied for similarity analysis.•Multidimensionality of the similarity space of DNA sequences is discussed.</description><subject>Algorithms</subject><subject>Animals</subject><subject>beta-Globins - genetics</subject><subject>Descriptors</subject><subject>Evolution, Molecular</subject><subject>Graphical representations of DNA sequences</subject><subject>Humans</subject><subject>Moments of inertia</subject><subject>Sequence Alignment - methods</subject><subject>Sequence Analysis, DNA - methods</subject><subject>Similarity/dissimilarity analysis of DNA sequences</subject><issn>0888-7543</issn><issn>1089-8646</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2014</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNqNkMtKAzEUhoMotlafQJBZupnxJJlcZiFS6hVK3eg6pJOMpMylJlNh3t7UVt2Jm3M48P3nhw-hcwwZBsyvVtnwZtsuI4DzDGQGGA7QGIMsUslzfojGIKVMBcvpCJ2EsAKAgkpyjEaEYUGZoGN0s-jaNPS6NdqbJLjG1dq7frgyLvxeiW51PQQXkq5KbhfTJNj3jW1LG07RUaXrYM_2e4Je7-9eZo_p_PnhaTadpyUD0adLwEteQAlGEMa4wLmMs5TAWMW5lVrQQlZSYFbwghsgXBRQ8cpqLoixhE7Q5e7v2nexOvSqcaG0da1b222CwjwXQGLsPyhlALkEGVG6Q0vfheBtpdbeNdoPCoPaSlYr9SVZbSUrkCpKjqmLfcFm2Vjzk_m2GoHrHWCjkQ9nvQql2-oyztuyV6ZzfxZ8Al40jJQ</recordid><startdate>20141201</startdate><enddate>20141201</enddate><creator>Wąż, Piotr</creator><creator>Bielińska-Wąż, Dorota</creator><general>Elsevier Inc</general><scope>6I.</scope><scope>AAFTH</scope><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7X8</scope><scope>7TM</scope><scope>8FD</scope><scope>FR3</scope><scope>P64</scope><scope>RC3</scope></search><sort><creationdate>20141201</creationdate><title>Non-standard similarity/dissimilarity analysis of DNA sequences</title><author>Wąż, Piotr ; Bielińska-Wąż, Dorota</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c507t-b01b690c0d725567148567c8055f66e8a7398f87159696d026790f6fea672de23</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2014</creationdate><topic>Algorithms</topic><topic>Animals</topic><topic>beta-Globins - genetics</topic><topic>Descriptors</topic><topic>Evolution, Molecular</topic><topic>Graphical representations of DNA sequences</topic><topic>Humans</topic><topic>Moments of inertia</topic><topic>Sequence Alignment - methods</topic><topic>Sequence Analysis, DNA - methods</topic><topic>Similarity/dissimilarity analysis of DNA sequences</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Wąż, Piotr</creatorcontrib><creatorcontrib>Bielińska-Wąż, Dorota</creatorcontrib><collection>ScienceDirect Open Access Titles</collection><collection>Elsevier:ScienceDirect:Open Access</collection><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>MEDLINE - Academic</collection><collection>Nucleic Acids Abstracts</collection><collection>Technology Research Database</collection><collection>Engineering Research Database</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>Genetics Abstracts</collection><jtitle>Genomics (San Diego, Calif.)</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Wąż, Piotr</au><au>Bielińska-Wąż, Dorota</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Non-standard similarity/dissimilarity analysis of DNA sequences</atitle><jtitle>Genomics (San Diego, Calif.)</jtitle><addtitle>Genomics</addtitle><date>2014-12-01</date><risdate>2014</risdate><volume>104</volume><issue>6</issue><spage>464</spage><epage>471</epage><pages>464-471</pages><issn>0888-7543</issn><eissn>1089-8646</eissn><abstract>Similarity/dissimilarity analysis of DNA sequences is performed using 3D-dynamic representation. The sequences are represented by material points in a 3D-space. Descriptors related to such 3D-dynamic graphs are calculated. A new normalized similarity measure is introduced for a comparison of the sequences. The method is applied to β-globin (HBB) genes of different species. Different methods are compared. The multidimensionality of similarity space of complex objects is discussed (different results for each of the methods). It is also shown that it is easier to find the properties which are consistent with the observation of the evolution of the species for the second exons of β-globin gene rather than for the first ones.
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| source | MEDLINE; Elektronische Zeitschriftenbibliothek - Frei zugängliche E-Journals; Access via ScienceDirect (Elsevier) |
| subjects | Algorithms Animals beta-Globins - genetics Descriptors Evolution, Molecular Graphical representations of DNA sequences Humans Moments of inertia Sequence Alignment - methods Sequence Analysis, DNA - methods Similarity/dissimilarity analysis of DNA sequences |
| title | Non-standard similarity/dissimilarity analysis of DNA sequences |
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