IDEAS home Printed from https://ideas.repec.org/a/eee/stapro/v61y2003i1p51-59.html
   My bibliography  Save this article

The exact distribution of the k-tuple statistic for sequence homology

Author

Listed:
  • Lou, W. Y. Wendy

Abstract

The distribution theory of runs and patterns has become increasingly useful in the field of biological sequence homology. One important application in detecting tandem duplications among DNA sequence segments is the k-tuple statistic Sn,k, the sum of matches in matching-runs of length k or longer in a sequence of n i.i.d. Bernoulli trials with success/matching probability p. Current approaches to this distribution problem are based on various approximations, due mainly to the numerical complexity of computing the exact distribution using a straightforward combinatorial approach. In this paper, we obtain a simple and efficient expression for the exact distribution of Sn,k using the principle of finite Markov chain imbedding. Our numerical results illustrate most importantly that for pattern lengths in the range n=10 to 100, a range commonly used in detecting DNA tandem repeats, the distribution, in general, is highly skewed and far from normal.

Suggested Citation

  • Lou, W. Y. Wendy, 2003. "The exact distribution of the k-tuple statistic for sequence homology," Statistics & Probability Letters, Elsevier, vol. 61(1), pages 51-59, January.
    • Handle: RePEc:eee:stapro:v:61:y:2003:i:1:p:51-59
    as

    Download full text from publisher

    File URL: http://www.sciencedirect.com/science/article/pii/S0167-7152(02)00337-1
    Download Restriction: Full text for ScienceDirect subscribers only
    ---><---

    As the access to this document is restricted, you may want to search for a different version of it.

    References listed on IDEAS

    as
    1. M. Koutras & V. Alexandrou, 1995. "Runs, scans and URN model distributions: A unified Markov chain approach," Annals of the Institute of Statistical Mathematics, Springer;The Institute of Statistical Mathematics, vol. 47(4), pages 743-766, December.
    Full references (including those not matched with items on IDEAS)

    Citations

    Citations are extracted by the CitEc Project, subscribe to its RSS feed for this item.
    as


    Cited by:

    1. Sotirios Bersimis & Athanasios Sachlas & Pantelis G. Bagos, 2017. "Discriminating membrane proteins using the joint distribution of length sums of success and failure runs," Statistical Methods & Applications, Springer;Società Italiana di Statistica, vol. 26(2), pages 251-272, June.
    2. Frosso Makri & Zaharias Psillakis, 2011. "On runs of length exceeding a threshold: normal approximation," Statistical Papers, Springer, vol. 52(3), pages 531-551, August.
    3. Arapis, Anastasios N. & Makri, Frosso S. & Psillakis, Zaharias M., 2016. "On the length and the position of the minimum sequence containing all runs of ones in a Markovian binary sequence," Statistics & Probability Letters, Elsevier, vol. 116(C), pages 45-54.
    4. Sáenz-de-Cabezón, Eduardo & Wynn, Henry P., 2011. "Computational algebraic algorithms for the reliability of generalized k-out-of-n and related systems," Mathematics and Computers in Simulation (MATCOM), Elsevier, vol. 82(1), pages 68-78.
    5. Donald E. K. Martin, 2005. "Distribution of the Number of Successes in Success Runs of Length at Least k in Higher-Order Markovian Sequences," Methodology and Computing in Applied Probability, Springer, vol. 7(4), pages 543-554, December.
    6. Serkan Eryilmaz, 2018. "Stochastic Ordering Among Success Runs Statistics in a Sequence of Exchangeable Binary Trials," Methodology and Computing in Applied Probability, Springer, vol. 20(2), pages 563-573, June.
    7. Makri, Frosso S. & Psillakis, Zaharias M. & Arapis, Anastasios N., 2015. "Length of the minimum sequence containing repeats of success runs," Statistics & Probability Letters, Elsevier, vol. 96(C), pages 28-37.
    8. Anastasios N. Arapis & Frosso S. Makri & Zaharias M. Psillakis, 2017. "Joint distribution of k-tuple statistics in zero-one sequences of Markov-dependent trials," Journal of Statistical Distributions and Applications, Springer, vol. 4(1), pages 1-13, December.
    9. Donald E. K. Martin & Laurent Noé, 2017. "Faster exact distributions of pattern statistics through sequential elimination of states," Annals of the Institute of Statistical Mathematics, Springer;The Institute of Statistical Mathematics, vol. 69(1), pages 231-248, February.
    10. M. Koutras & S. Bersimis & D. Antzoulakos, 2008. "Bivariate Markov chain embeddable variables of polynomial type," Annals of the Institute of Statistical Mathematics, Springer;The Institute of Statistical Mathematics, vol. 60(1), pages 173-191, March.

    Most related items

    These are the items that most often cite the same works as this one and are cited by the same works as this one.
    1. Serkan Eryilmaz, 2005. "On the distribution and expectation of success runs in nonhomogeneous Markov dependent trials," Statistical Papers, Springer, vol. 46(1), pages 117-128, January.
    2. Markos V. Koutras & Demetrios P. Lyberopoulos, 2018. "Asymptotic results for jump probabilities associated to the multiple scan statistic," Annals of the Institute of Statistical Mathematics, Springer;The Institute of Statistical Mathematics, vol. 70(5), pages 951-968, October.
    3. Stathis Chadjiconstantinidis & Serkan Eryilmaz, 2023. "Computing waiting time probabilities related to $$ (k_{1},k_{2},\ldots ,k_{l})$$ ( k 1 , k 2 , … , k l ) pattern," Statistical Papers, Springer, vol. 64(5), pages 1373-1390, October.
    4. Kiyoshi Inoue & Sigeo Aki, 2013. "Distributions of numbers of runs and scans on directed acyclic graphs with generation," Computational Statistics, Springer, vol. 28(3), pages 1133-1150, June.
    5. Yong Kong, 2019. "Decoupling Combinatorial Complexity: a Two-Step Approach to Distributions of Runs," Methodology and Computing in Applied Probability, Springer, vol. 21(3), pages 789-803, September.
    6. Spiros D. Dafnis & Frosso S. Makri, 2023. "Distributions Related to Weak Runs With a Minimum and a Maximum Number of Successes: A Unified Approach," Methodology and Computing in Applied Probability, Springer, vol. 25(1), pages 1-24, March.
    7. A. Godbole & M. Koutras & F. Milienos, 2011. "Binary consecutive covering arrays," Annals of the Institute of Statistical Mathematics, Springer;The Institute of Statistical Mathematics, vol. 63(3), pages 559-584, June.
    8. Yi-Shen Lin & Xenos Chang-Shuo Lin & Daniel Wei-Chung Miao & Yi-Ching Yao, 2020. "Corrected Discrete Approximations for Multiple Window Scan Statistics of One-Dimensional Poisson Processes," Methodology and Computing in Applied Probability, Springer, vol. 22(1), pages 237-265, March.
    9. Spiros D. Dafnis & Frosso S. Makri, 2022. "Weak runs in sequences of binary trials," Metrika: International Journal for Theoretical and Applied Statistics, Springer, vol. 85(5), pages 573-603, July.
    10. Kiyoshi Inoue & Sigeo Aki, 2003. "Generalized binomial and negative binomial distributions of orderk by thel-overlapping enumeration scheme," Annals of the Institute of Statistical Mathematics, Springer;The Institute of Statistical Mathematics, vol. 55(1), pages 153-167, March.
    11. Bartolucci, F., 2001. "Developments of the Markov chain approach within the distribution theory of runs," Computational Statistics & Data Analysis, Elsevier, vol. 36(1), pages 107-118, March.
    12. Aki, Sigeo, 2008. "Joint distributions of numbers of occurrences of a discrete pattern and weak convergence of an empirical process for the pattern," Journal of Multivariate Analysis, Elsevier, vol. 99(7), pages 1460-1473, August.
    13. Bobotas, Panayiotis & Koutras, Markos V., 2019. "Distributions of the minimum and the maximum of a random number of random variables," Statistics & Probability Letters, Elsevier, vol. 146(C), pages 57-64.
    14. Inoue, Kiyoshi & Aki, Sigeo, 2010. "On the conditional and unconditional distributions of the number of success runs on a circle with applications," Statistics & Probability Letters, Elsevier, vol. 80(9-10), pages 874-885, May.
    15. Spiros Dafnis & Andreas Philippou & Demetrios Antzoulakos, 2012. "Distributions of patterns of two successes separated by a string of k-2 failures," Statistical Papers, Springer, vol. 53(2), pages 323-344, May.
    16. Dafnis, Spiros D. & Makri, Frosso S. & Philippou, Andreas N., 2019. "The reliability of a generalized consecutive system," Applied Mathematics and Computation, Elsevier, vol. 359(C), pages 186-193.
    17. G. Nuel, 2019. "Moments of the Count of a Regular Expression in a Heterogeneous Random Sequence," Methodology and Computing in Applied Probability, Springer, vol. 21(3), pages 875-887, September.
    18. Kiyoshi Inoue & Sigeo Aki, 2018. "Joint distributions of numbers of runs of specified lengths on directed trees," Statistical Papers, Springer, vol. 59(1), pages 249-269, March.
    19. Qing Han & Sigeo Aki, 1999. "Joint Distributions of Runs in a Sequence of Multi-State Trials," Annals of the Institute of Statistical Mathematics, Springer;The Institute of Statistical Mathematics, vol. 51(3), pages 419-447, September.
    20. Kiyoshi Inoue & Sigeo Aki, 2011. "Bivariate Fibonacci polynomials of order k with statistical applications," Annals of the Institute of Statistical Mathematics, Springer;The Institute of Statistical Mathematics, vol. 63(1), pages 197-210, February.

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:eee:stapro:v:61:y:2003:i:1:p:51-59. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    If CitEc recognized a bibliographic reference but did not link an item in RePEc to it, you can help with this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: Catherine Liu (email available below). General contact details of provider: http://www.elsevier.com/wps/find/journaldescription.cws_home/622892/description#description .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.