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  CorGen-measuring and generating long-range correlations for DNA sequence analysis

Messer, P. W., & Arndt, P. F. (2006). CorGen-measuring and generating long-range correlations for DNA sequence analysis. Nucleic Acids Research, 34, W692-W695. doi:10.1093/nar/gkl234.

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Genre: Journal Article
Alternative Title : Nucleic Acids Res.

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 Creators:
Messer, Philipp W.1, Author
Arndt, Peter F.2, Author              
Affiliations:
1Max Planck Society, ou_persistent13              
2Evolutionary 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: CorGen is a web server that measures long-range correlations in the base composition of DNA and generates random sequences with the same correlation parameters. Long-range correlations are characterized by a power-law decay of the auto correlation function of the GC-content. The widespread presence of such correlations in eukaryotic genomes calls for their incorporation into accurate null models of eukaryotic DNA in computational biology. For example, the score statistics of sequence alignment and the performance of motif finding algorithms are significantly affected by the presence of genomic long-range correlations. We use an expansion-randomization dynamics to efficiently generate the correlated random sequences. The server is available at http://corgen.molgen.mpg.de

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Language(s): eng - English
 Dates: 2006-03-28
 Publication Status: Published in print
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 Identifiers: eDoc: 311239
DOI: 10.1093/nar/gkl234
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Title: Nucleic Acids Research
  Alternative Title : Nucleic Acids Res.
Source Genre: Journal
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Pages: - Volume / Issue: 34 Sequence Number: - Start / End Page: W692 - W695 Identifier: ISSN: 0301-5610