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Bioinformatics Advance Access originally published online on March 15, 2005
Bioinformatics 2005 21(10):2322-2328; doi:10.1093/bioinformatics/bti376
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© The Author 2005. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions{at}oupjournals.org

Identification and measurement of neighbor-dependent nucleotide substitution processes

Peter F. Arndt 1,* and Terence Hwa 2

1Max Planck Institute for Molecular Genetics Ihnestrasse 73, 14195 Berlin, Germany
2Physics Department and Center for Theoretical Biological Physics UC San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0374, USA

*To whom correspondence should be addressed.

Motivation: Neighbor-dependent substitution processes generated specific pattern of dinucleotide frequencies in the genomes of most organisms. The CpG-methylation–deamination process is, e.g. a prominent process in vertebrates (CpG effect). Such processes, often with unknown mechanistic origins, need to be incorporated into realistic models of nucleotide substitutions.

Results: Based on a general framework of nucleotide substitutions we developed a method that is able to identify the most relevant neighbor-dependent substitution processes, estimate their relative frequencies and judge their importance in order to be included into the modeling. Starting from a model for neighbor independent nucleotide substitution we successively added neighbor-dependent substitution processes in the order of their ability to increase the likelihood of the model describing given data. The analysis of neighbor-dependent nucleotide substitutions based on repetitive elements found in the genomes of human, zebrafish and fruit fly is presented.

Availability: A web server to perform the presented analysis is freely available at: http://evogen.molgen.mpg.de/server/substitution-analysis

Contact: arndt{at}molgen.mpg.de


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