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Nucleic Acids Research 2006 34(Web Server issue):W692-W695; doi:10.1093/nar/gkl234
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© The Author 2006. Published by Oxford University Press. All rights reserved
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Article

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

Philipp W. Messer* and Peter F. Arndt

Max Planck Institute for Molecular Genetics Ihnestrasse 73, 14195 Berlin, Germany

*To whom correspondence should be addressed. Tel: +49 30 8413 1161; Fax: +49 30 8413 1152; Email: philipp.messer{at}molgen.mpg.de

Received February 14, 2006. Revised March 1, 2006. Accepted March 28, 2006.

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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