A probabilistic measure for alignment-free sequence comparison
Motivation: Alignment-free sequence comparison methods are still in the early stages of development compared to those of alignment-based sequence analysis. In this paper, we introduce a probabilistic measure of similarity between two biological sequences without alignment. The method is based on the...
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| Veröffentlicht in: | Bioinformatics 2004-12, Vol.20 (18), p.3455-3461 |
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| creator | Pham, Tuan D. Zuegg, Johannes |
| description | Motivation: Alignment-free sequence comparison methods are still in the early stages of development compared to those of alignment-based sequence analysis. In this paper, we introduce a probabilistic measure of similarity between two biological sequences without alignment. The method is based on the concept of comparing the similarity/dissimilarity between two constructed Markov models. Results: The method was tested against six DNA sequences, which are the thrA, thrB and thrC genes of the threonine operons from Escherichia coli K-12 and from Shigella flexneri; and one random sequence having the same base composition as thrA from E.coli. These results were compared with those obtained from CLUSTAL W algorithm (alignment-based) and the chaos game representation (alignment-free). The method was further tested against a more complex set of 40 DNA sequences and compared with other existing sequence similarity measures (alignment-free). Availability: All datasets and computer codes written in MATLAB are available upon request from the first author. |
| doi_str_mv | 10.1093/bioinformatics/bth426 |
| format | Article |
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In this paper, we introduce a probabilistic measure of similarity between two biological sequences without alignment. The method is based on the concept of comparing the similarity/dissimilarity between two constructed Markov models. Results: The method was tested against six DNA sequences, which are the thrA, thrB and thrC genes of the threonine operons from Escherichia coli K-12 and from Shigella flexneri; and one random sequence having the same base composition as thrA from E.coli. These results were compared with those obtained from CLUSTAL W algorithm (alignment-based) and the chaos game representation (alignment-free). The method was further tested against a more complex set of 40 DNA sequences and compared with other existing sequence similarity measures (alignment-free). 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Data processing in biology (general aspects) ; Models, Genetic ; Models, Statistical ; Operon - genetics ; Sequence Alignment - methods ; Sequence Analysis, DNA - methods ; Sequence Homology, Nucleic Acid ; Shigella flexneri ; Shigella flexneri - genetics ; Threonine - genetics</subject><ispartof>Bioinformatics, 2004-12, Vol.20 (18), p.3455-3461</ispartof><rights>2005 INIST-CNRS</rights><rights>Copyright Oxford University Press(England) Dec 12, 2004</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c546t-333e45c7c75916d1b8303c38d2ba5c6723b99d1167442519cf58c2f7b95823013</citedby></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><link.rule.ids>314,780,784,27924,27925</link.rule.ids><backlink>$$Uhttp://pascal-francis.inist.fr/vibad/index.php?action=getRecordDetail&idt=16404863$$DView record in Pascal Francis$$Hfree_for_read</backlink><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/15271780$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Pham, Tuan D.</creatorcontrib><creatorcontrib>Zuegg, Johannes</creatorcontrib><title>A probabilistic measure for alignment-free sequence comparison</title><title>Bioinformatics</title><addtitle>Bioinformatics</addtitle><description>Motivation: Alignment-free sequence comparison methods are still in the early stages of development compared to those of alignment-based sequence analysis. In this paper, we introduce a probabilistic measure of similarity between two biological sequences without alignment. The method is based on the concept of comparing the similarity/dissimilarity between two constructed Markov models. Results: The method was tested against six DNA sequences, which are the thrA, thrB and thrC genes of the threonine operons from Escherichia coli K-12 and from Shigella flexneri; and one random sequence having the same base composition as thrA from E.coli. These results were compared with those obtained from CLUSTAL W algorithm (alignment-based) and the chaos game representation (alignment-free). The method was further tested against a more complex set of 40 DNA sequences and compared with other existing sequence similarity measures (alignment-free). 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Data processing in biology (general aspects)</subject><subject>Models, Genetic</subject><subject>Models, Statistical</subject><subject>Operon - genetics</subject><subject>Sequence Alignment - methods</subject><subject>Sequence Analysis, DNA - methods</subject><subject>Sequence Homology, Nucleic Acid</subject><subject>Shigella flexneri</subject><subject>Shigella flexneri - genetics</subject><subject>Threonine - genetics</subject><issn>1367-4803</issn><issn>1460-2059</issn><issn>1367-4811</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2004</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNqFkUtLAzEUhYMoWh8_QRkE3Y3mncxGENFWKVioorgJSZrR6DxqMgP67420WHTj6gbudw735ACwj-AJggU5Nb71TdmGWnfexlPTvVDM18AAUQ5zDFmxnt6Ei5xKSLbAdoyvEDJEKd0EW4hhgYSEA3B2ns1Da7TxlY_JKaudjn1wWbLOdOWfm9o1XV4G57Lo3nvXWJfZtp7r4GPb7IKNUlfR7S3nDri_ury7GOXj2-H1xfk4t4zyLieEOMqssIIViM-QkQQSS-QMG80sF5iYopghxAWlmKHClkxaXApTMIkJRGQHHC9807HpiNip2kfrqko3ru2j4ikOS-p_QQwhh5LxBB7-AV_bPjQphEKF5IkQMEFsAdnQxhhcqebB1zp8KgTVdw3qdw1qUUPSHSzNe1O72Uq1_PcEHC0BHa2uyqAb6-OK4xRSyUni8gWXynEfP3sd3lJkIpgaPT6p6WQywdPhjXogXwrXo2A</recordid><startdate>20041212</startdate><enddate>20041212</enddate><creator>Pham, Tuan D.</creator><creator>Zuegg, Johannes</creator><general>Oxford University Press</general><general>Oxford Publishing Limited (England)</general><scope>BSCLL</scope><scope>IQODW</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>7QF</scope><scope>7QO</scope><scope>7QQ</scope><scope>7SC</scope><scope>7SE</scope><scope>7SP</scope><scope>7SR</scope><scope>7TA</scope><scope>7TB</scope><scope>7TM</scope><scope>7TO</scope><scope>7U5</scope><scope>8BQ</scope><scope>8FD</scope><scope>F28</scope><scope>FR3</scope><scope>H8D</scope><scope>H8G</scope><scope>H94</scope><scope>JG9</scope><scope>JQ2</scope><scope>K9.</scope><scope>KR7</scope><scope>L7M</scope><scope>L~C</scope><scope>L~D</scope><scope>P64</scope><scope>7QL</scope><scope>C1K</scope><scope>7X8</scope></search><sort><creationdate>20041212</creationdate><title>A probabilistic measure for alignment-free sequence comparison</title><author>Pham, Tuan D. ; Zuegg, Johannes</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c546t-333e45c7c75916d1b8303c38d2ba5c6723b99d1167442519cf58c2f7b95823013</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2004</creationdate><topic>Algorithms</topic><topic>Biological and medical sciences</topic><topic>Computer Simulation</topic><topic>Escherichia coli</topic><topic>Escherichia coli - genetics</topic><topic>Fundamental and applied biological sciences. Psychology</topic><topic>General aspects</topic><topic>Mathematics in biology. Statistical analysis. Models. Metrology. 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In this paper, we introduce a probabilistic measure of similarity between two biological sequences without alignment. The method is based on the concept of comparing the similarity/dissimilarity between two constructed Markov models. Results: The method was tested against six DNA sequences, which are the thrA, thrB and thrC genes of the threonine operons from Escherichia coli K-12 and from Shigella flexneri; and one random sequence having the same base composition as thrA from E.coli. These results were compared with those obtained from CLUSTAL W algorithm (alignment-based) and the chaos game representation (alignment-free). The method was further tested against a more complex set of 40 DNA sequences and compared with other existing sequence similarity measures (alignment-free). Availability: All datasets and computer codes written in MATLAB are available upon request from the first author.</abstract><cop>Oxford</cop><pub>Oxford University Press</pub><pmid>15271780</pmid><doi>10.1093/bioinformatics/bth426</doi><tpages>7</tpages><oa>free_for_read</oa></addata></record> |
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| subjects | Algorithms Biological and medical sciences Computer Simulation Escherichia coli Escherichia coli - genetics Fundamental and applied biological sciences. Psychology General aspects Mathematics in biology. Statistical analysis. Models. Metrology. Data processing in biology (general aspects) Models, Genetic Models, Statistical Operon - genetics Sequence Alignment - methods Sequence Analysis, DNA - methods Sequence Homology, Nucleic Acid Shigella flexneri Shigella flexneri - genetics Threonine - genetics |
| title | A probabilistic measure for alignment-free sequence comparison |
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