Summary: BIOINFORMATICS ORIGINAL PAPER
Vol. 21 no. 10 2005, pages 2322­2328
doi:10.1093/bioinformatics/bti376
Phylogenetics
Identification and measurement of neighbor-dependent
nucleotide substitution processes
Peter F. Arndt1, and Terence Hwa2
1Max Planck Institute for Molecular Genetics, Ihnestrasse 73, 14195 Berlin, Germany and 2Physics Department
and Center for Theoretical Biological Physics, UC San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0374, USA
Received on November 17, 2004; revised on February 16, 2005; accepted on March 4, 2005
Advance Access publication March 15, 2005
ABSTRACT
Motivation: Neighbor-dependent substitution processes generated
specific pattern of dinucleotide frequencies in the genomes of most
organisms. The CpG-methylation­deamination 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-

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