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  Effects of Long-Range Correlations in DNA on Sequence Alignment Score Statistics.

Messer, P. W., Bundschuh, R., Vingron, M., & Arndt, P. F. (2007). Effects of Long-Range Correlations in DNA on Sequence Alignment Score Statistics. Journal of Computational Biology: A Journal of Computational Molecular Cell Biology, 14(5), 655-668. doi:10.1089/cmb.2007.R008.

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Genre: Journal Article
Alternative Title : CMB

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 Creators:
Messer, Philipp W.1, Author
Bundschuh, Ralf, Author
Vingron, Martin2, Author              
Arndt, Peter F.3, Author              
Affiliations:
1Max Planck Society, ou_persistent13              
2Gene regulation (Martin Vingron), Dept. of Computational Molecular Biology (Head: Martin Vingron), Max Planck Institute for Molecular Genetics, Max Planck Society, ou_1479639              
3Evolutionary Genomics (Peter Arndt), Dept. of Computational Molecular Biology (Head: Martin Vingron), Max Planck Institute for Molecular Genetics, Max Planck Society, ou_1479638              

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 Abstract: Long-range correlations in genomic base composition are a ubiquitous statistical feature among many eukaryotic genomes. In this article, these correlations are shown to substantially influence the statistics of sequence alignment scores. Using a Gaussian approximation to model the correlated score landscape, we calculate the corrections to the scale parameter lambda of the extreme value distribution of alignment scores. Our approximate analytic results are supported by a detailed numerical study based on a simple algorithm to efficiently generate long-range correlated random sequences. We find both, mean and exponential tail of the score distribution for long-range correlated sequences to be substantially shifted compared to random sequences with independent nucleotides. The significance of measured alignment scores will therefore change upon incorporation of the correlations in the null model. We discuss the magnitude of this effect in a biological context.

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Language(s): eng - English
 Dates: 2007-06-01
 Publication Status: Published in print
 Pages: -
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 Table of Contents: -
 Rev. Type: -
 Identifiers: eDoc: 336947
DOI: 10.1089/cmb.2007.R008.
 Degree: -

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Title: Journal of Computational Biology : A Journal of Computational Molecular Cell Biology
  Alternative Title : CMB
Source Genre: Journal
 Creator(s):
Affiliations:
Publ. Info: -
Pages: - Volume / Issue: 14 (5) Sequence Number: - Start / End Page: 655 - 668 Identifier: ISSN: 1066-5277