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Statistical Applications in Genetics and Molecular Biology

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1544-6115
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Volume 9, Issue 1 (Jul 2010)

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Confidently Estimating the Number of DNA Replication Origins

Anand Bhaskar
  • Computer Science Division, University of California, Berkeley
/ Uri Keich
  • School of Mathematics and Statistics, University of Sydney
Published Online: 2010-07-02 | DOI: https://doi.org/10.2202/1544-6115.1544

We present a method for estimating and providing a confidence interval for the number of DNA replication origins in the genome of the yeast Kluyveromyces lactis. The method requires an initial set of verified sites from which a position specific frequency matrix (PSFM) can be constructed. We further assume that we have access to a sparingly used experimental procedure which can verify the functionality of a few, but not all, computationally predicted sites. While our motivation comes from estimating the number of autonomously replicating sequences (ARSs), our method can also be applied to estimating the genome-wide number of “functional” transcription factor binding sites, where functionality is determined by experimental verification of the transcription factor binding event using, for example, ChIP data. The reliability of our method is demonstrated by correctly predicting the known number of Saccharomyces cerevisiae ARSs as well as the number of S. cerevisiae probes that bind to the transcription factor ABF1.

Keywords: PSFM; confidence interval; ARS; K. lactis; S. cerevisiae

About the article

Published Online: 2010-07-02



Citation Information: Statistical Applications in Genetics and Molecular Biology, ISSN (Online) 1544-6115, DOI: https://doi.org/10.2202/1544-6115.1544. Export Citation

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