Model of perfect tandem repeat with random pattern and empirical homogeneity testing poly-criteria for latent periodicity revelation in biological sequences
A model of perfect tandem repeat with random pattern has been considered. It expands a notion of approximate tandem repeat and describes new kind of latent periodicity in biological sequences, which has been named profile periodicity. Based on this model, an original spectral–statistical approach ha...
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| Veröffentlicht in: | Mathematical biosciences 2008, Vol.211 (1), p.186-204 |
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| creator | Chaley, Maria Kutyrkin, Vladimir |
| description | A model of perfect tandem repeat with random pattern has been considered. It expands a notion of approximate tandem repeat and describes new kind of latent periodicity in biological sequences, which has been named profile periodicity. Based on this model, an original spectral–statistical approach has been proposed for the estimation of size of the periodicity pattern in sequences of approximate tandem repeats. In contrast to existing approaches, this is applicable in practical conditions of unrepresentative samples (for standard criteria). This approach is suitable and effective for preliminary automated revelation of latent periodicity. The advantages of the spectral–statistical approach to estimation of the periodicity pattern for approximate tandem repeats have been demonstrated in comparison with the other methods. |
| doi_str_mv | 10.1016/j.mbs.2007.10.008 |
| format | Article |
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It expands a notion of approximate tandem repeat and describes new kind of latent periodicity in biological sequences, which has been named profile periodicity. Based on this model, an original spectral–statistical approach has been proposed for the estimation of size of the periodicity pattern in sequences of approximate tandem repeats. In contrast to existing approaches, this is applicable in practical conditions of unrepresentative samples (for standard criteria). This approach is suitable and effective for preliminary automated revelation of latent periodicity. The advantages of the spectral–statistical approach to estimation of the periodicity pattern for approximate tandem repeats have been demonstrated in comparison with the other methods.</description><identifier>ISSN: 0025-5564</identifier><identifier>EISSN: 1879-3134</identifier><identifier>DOI: 10.1016/j.mbs.2007.10.008</identifier><identifier>PMID: 18062999</identifier><language>eng</language><publisher>United States: Elsevier Inc</publisher><subject>Algorithms ; Animals ; Base Sequence ; Caenorhabditis elegans - genetics ; Databases, Genetic ; Latent periodicity ; Models, Genetic ; Molecular Sequence Data ; Pattern Recognition, Automated - methods ; Profile matrix ; Sequence Analysis, DNA - methods ; Sequence Homology, Nucleic Acid ; Spectrum of heterogeneity manifestations ; Stochastic Processes ; Tandem Repeat Sequences - genetics ; Test-period</subject><ispartof>Mathematical biosciences, 2008, Vol.211 (1), p.186-204</ispartof><rights>2007 Elsevier Inc.</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c382t-ebf45c75d9d1b0a2d1c2d1b8c0a54a9b30904d23021807ef21f98362789c7643</citedby><cites>FETCH-LOGICAL-c382t-ebf45c75d9d1b0a2d1c2d1b8c0a54a9b30904d23021807ef21f98362789c7643</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktohtml>$$Uhttps://www.sciencedirect.com/science/article/pii/S0025556407002118$$EHTML$$P50$$Gelsevier$$H</linktohtml><link.rule.ids>314,776,780,3537,4010,27900,27901,27902,65306</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/18062999$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Chaley, Maria</creatorcontrib><creatorcontrib>Kutyrkin, Vladimir</creatorcontrib><title>Model of perfect tandem repeat with random pattern and empirical homogeneity testing poly-criteria for latent periodicity revelation in biological sequences</title><title>Mathematical biosciences</title><addtitle>Math Biosci</addtitle><description>A model of perfect tandem repeat with random pattern has been considered. It expands a notion of approximate tandem repeat and describes new kind of latent periodicity in biological sequences, which has been named profile periodicity. Based on this model, an original spectral–statistical approach has been proposed for the estimation of size of the periodicity pattern in sequences of approximate tandem repeats. In contrast to existing approaches, this is applicable in practical conditions of unrepresentative samples (for standard criteria). This approach is suitable and effective for preliminary automated revelation of latent periodicity. 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| ispartof | Mathematical biosciences, 2008, Vol.211 (1), p.186-204 |
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| language | eng |
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| source | MEDLINE; Elsevier ScienceDirect Journals |
| subjects | Algorithms Animals Base Sequence Caenorhabditis elegans - genetics Databases, Genetic Latent periodicity Models, Genetic Molecular Sequence Data Pattern Recognition, Automated - methods Profile matrix Sequence Analysis, DNA - methods Sequence Homology, Nucleic Acid Spectrum of heterogeneity manifestations Stochastic Processes Tandem Repeat Sequences - genetics Test-period |
| title | Model of perfect tandem repeat with random pattern and empirical homogeneity testing poly-criteria for latent periodicity revelation in biological sequences |
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