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

Summary: 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
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 cor-
relation parameters. Long-range correlations are
characterized by a power-law decay of the auto
correlation function of the GC-content. The wide-
spread presence of such correlations in eukaryotic
genomes calls for their incorporation into accurate
null models of eukaryotic DNA in computational bio-
logy. For example, the score statistics of sequence
alignment and the performance of motif finding algo-
rithms are significantly affected by the presence
of genomic long-range correlations. We use an
expansion-randomization dynamics to efficiently


Source: Arndt, Peter - Max-Planck-Institut für molekulare Genetik
Spang, Rainer - Computational Molecular Biology Group, Max-Planck-Institut für molekulare Genetik


Collections: Biology and Medicine; Biotechnology; Computer Technologies and Information Sciences; Physics