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  1. Article ; Online: An Asymmetric Alignment Algorithm for Estimating Ancestor-Descendant Edit Distance for Tandem Repeats.

    Matroud, Atheer / Tuffley, Christopher / Hendy, Michael

    IEEE/ACM transactions on computational biology and bioinformatics

    2022  Volume 19, Issue 4, Page(s) 2080–2091

    Abstract: Tandem repeats are repetitive structures present in some DNA sequences, consisting of many repeated copies of a single motif. They can serve as important markers for phylogenetic and population genetic studies, due to the high polymorphism in the number ... ...

    Abstract Tandem repeats are repetitive structures present in some DNA sequences, consisting of many repeated copies of a single motif. They can serve as important markers for phylogenetic and population genetic studies, due to the high polymorphism in the number of motif copies as well as variations in the motif. The first step in using tandem repeats for phylogenetic studies is to estimate the evolutionary distance between a pair D
    MeSH term(s) Algorithms ; Biological Evolution ; Phylogeny ; Tandem Repeat Sequences/genetics
    Language English
    Publishing date 2022-08-08
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ISSN 1557-9964
    ISSN (online) 1557-9964
    DOI 10.1109/TCBB.2021.3059239
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Book ; Online: Parametric study of E. coli incidence with reference to the New Zealand freshwater standards and the Manawat\=u-Whanganui region

    Marsland, Stephen R / McLachlan, Robert I / Tuffley, Christopher

    2021  

    Abstract: The New Zealand National Policy Statement for Freshwater Management 2020 sets several targets for freshwater quality, six of which are measurements of rivers; others relate to lakes. Each regional council is required to monitor freshwater quality and to ... ...

    Abstract The New Zealand National Policy Statement for Freshwater Management 2020 sets several targets for freshwater quality, six of which are measurements of rivers; others relate to lakes. Each regional council is required to monitor freshwater quality and to respond as prescribed in order to meet the targets. One target of particular public interest is based on four criteria determined from recent E. coli readings, and concerns the health risk of swimming in a river. However, the inherent variability of the data makes it difficult to determine the water quality state and trend reliably, particularly using traditional methods based on percentiles. Therefore, in this study we return to the parametric lognormal model of E. coli distribution, from which the official criteria were developed. We interpret the classification system in terms of the parametric model and show that the parametric model can reduce uncertainty and can incorporate more useful information, especially from very high E. coli readings, and is suitable for censored data. We apply the parametric model for state and trend to 135 sites in the Manawat\=u-Whanganui region.
    Keywords Statistics - Applications ; Physics - Data Analysis ; Statistics and Probability ; 62P12
    Subject code 910
    Publishing date 2021-10-04
    Publishing country us
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  3. Article ; Online: An algorithm to solve the motif alignment problem for approximate nested tandem repeats in biological sequences.

    Matroud, Atheer A / Tuffley, Christopher P / Hendy, Michael D

    Journal of computational biology : a journal of computational molecular cell biology

    2011  Volume 18, Issue 9, Page(s) 1211–1218

    Abstract: An approximate nested tandem repeat (NTR) in a string T is a complex repetitive structure consisting of many approximate copies of two substrings x and X ("motifs") interspersed with one another. NTRs fall into a class of repetitive structures broadly ... ...

    Abstract An approximate nested tandem repeat (NTR) in a string T is a complex repetitive structure consisting of many approximate copies of two substrings x and X ("motifs") interspersed with one another. NTRs fall into a class of repetitive structures broadly known as subrepeats. NTRs have been found in real DNA sequences and are expected to be important in evolutionary biology, both in understanding evolution of the ribosomal DNA (where NTRs can occur), and as a potential marker in population genetic and phylogenetic studies. This article describes an alignment algorithm for the verification phase of the software tool NTRFinder developed for database searches for NTRs. When the search algorithm has located a subsequence containing a possible NTR, with motifs X and x, a verification step aligns this subsequence against an exact NTR built from the templates X and x, to determine whether the subsequence contains an approximate NTR and its extent. This article describes an algorithm to solve this alignment problem in O(|T|(|X| + |x|)) space and time. The algorithm is based on Fischetti et al.'s wrap-around dynamic programming.
    MeSH term(s) Algorithms ; Data Mining/methods ; Sequence Alignment/methods ; Sequence Analysis, DNA/methods ; Tandem Repeat Sequences
    Language English
    Publishing date 2011-09
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2030900-4
    ISSN 1557-8666 ; 1066-5277
    ISSN (online) 1557-8666
    ISSN 1066-5277
    DOI 10.1089/cmb.2011.0101
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Correcting the apparent mutation rate acceleration at shorter time scales under a Jukes-Cantor model.

    Tuffley, Christopher / Timothy, W / White, J / Hendy, Michael D / Penny, David

    Molecular biology and evolution

    2012  Volume 29, Issue 12, Page(s) 3703–3709

    Abstract: At macroevolutionary time scales, and for a constant mutation rate, there is an expected linear relationship between time and the number of inferred neutral mutations (the "molecular clock"). However, at shorter time scales, a number of recent studies ... ...

    Abstract At macroevolutionary time scales, and for a constant mutation rate, there is an expected linear relationship between time and the number of inferred neutral mutations (the "molecular clock"). However, at shorter time scales, a number of recent studies have observed an apparent acceleration in the rate of molecular evolution. We study this apparent acceleration under a Jukes-Cantor model applied to a randomly mating population, and show that, under the model, it arises as a consequence of ignoring short-term effects due to existing diversity within the population. The acceleration can be accounted for by adding the correction term h(0)e(-4μt/3) to the usual Jukes-Cantor formula p(t) = 3/4(1 - e (-(-4μt/3), where h(0) is the expected heterozygosity in the population at time t = 0. The true mutation rate μ may then be recovered, even if h(0) is not known, by estimating μ and h(0) simultaneously using least squares. Rate estimates made without the correction term (i.e., incorrectly assuming the population to be homogeneous) will result in a divergent rate curve of the form μ(div) = μ + C/t, so that the mutation rate appears to approach infinity as the time scale approaches zero. Although our quantitative results apply only to the Jukes-Cantor model, it is reasonable to suppose that the qualitative picture that emerges also applies to more complex models. Our study, therefore, demonstrates the importance of properly accounting for any ancestral diversity, because it may otherwise play a dominant role in rate overestimation.
    MeSH term(s) Evolution, Molecular ; Genetic Variation ; Genetics, Population/methods ; Heterozygote ; Models, Genetic ; Mutation Rate ; Time Factors
    Language English
    Publishing date 2012-12
    Publishing country United States
    Document type Journal Article
    ZDB-ID 998579-7
    ISSN 1537-1719 ; 0737-4038
    ISSN (online) 1537-1719
    ISSN 0737-4038
    DOI 10.1093/molbev/mss172
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  5. Book ; Online: Correcting the apparent mutation rate acceleration at shorter time scales under a Jukes-Cantor model

    Tuffley, Christopher / White, Timothy / Hendy, Michael D. / Penny, David

    2011  

    Abstract: At macroevolutionary time scales, and for a constant mutation rate, there is an expected linear relationship between time and the number of inferred neutral mutations (the "molecular clock"). However, at shorter time scales a number of recent studies ... ...

    Abstract At macroevolutionary time scales, and for a constant mutation rate, there is an expected linear relationship between time and the number of inferred neutral mutations (the "molecular clock"). However, at shorter time scales a number of recent studies have observed an apparent acceleration in the rate of molecular evolution. We study this apparent acceleration under a Jukes-Cantor model applied to a randomly mating population, and show that, under the model, it arises as a consequence of ignoring short term effects due to existing diversity within the population. The acceleration can be accounted for by adding the correction term h_0e^{-4mu*t/3} to the usual Jukes-Cantor formula p(t)=(3/4)(1-e^{-4mu*t/3}), where h_0 is the expected heterozygosity in the population at time t=0. The true mutation rate mu may then be recovered, even if h_0 is not known, by estimating mu and h_0 simultaneously using least squares. Rate estimates made without the correction term (that is, incorrectly assuming the population to be homogeneous) will result in a divergent rate curve of the form mu_{div}=mu+C/t, so that the mutation rate appears to approach infinity as the time scale approaches zero. While our quantitative results apply only to the Jukes-Cantor model, it is reasonable to suppose that the qualitative picture that emerges also applies to more complex models. Our study therefore demonstrates the importance of properly accounting for any ancestral diversity, as it may otherwise play a dominant role in rate overestimation.

    Comment: LaTeX; 11 pages, 3 graphs. v3: Typoes corrected, including some in formulae. v2: Abstract, introduction and conclusions significantly rewritten to better reflect and explain the significance of the results
    Keywords Quantitative Biology - Populations and Evolution ; 92D15
    Subject code 612
    Publishing date 2011-12-19
    Publishing country us
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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