Skip Navigation



Bioinformatics Advance Access published online on March 15, 2005
Bioinformatics, doi:10.1093/bioinformatics/bti376
This Article
Right arrow Advance Access manuscript (PDF) Freely available
Right arrow Supplementary data
Right arrow All Versions of this Article:
21/10/2322    most recent
bti376v1
Right arrow Comments: Submit a response
Right arrow Alert me when this article is cited
Right arrow Alert me when Comments are posted
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrowRequest Permissions
Google Scholar
Right arrow Articles by Arndt, P. F.
Right arrow Articles by Hwa, T.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Arndt, P. F.
Right arrow Articles by Hwa, T.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

© The Author (2005). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oupjournals.org
Received November 17, 2004
Revised February 16, 2005
Accepted March 4, 2005

Article

Identification and measurement of neighbor dependent nucleotide substitution processes

Peter F. Arndt 1* and Terence Hwa 2

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

* To whom correspondence should be addressed.
Peter F. Arndt, E-mail: arndt{at}molgen.mpg.de


  Abstract

Motivation: Neighbor dependent substitution processes generated specific pattern of dinucleotide frequencies in the genomes of most organisms. The CpG-methylation-deamination process is, for example, 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 develop a method that is able to identify the most relevant neighbor dependent substitution processes, estimate their relative frequencies, and judge their importance to be included into the modeling. Starting from a model for neighbor independent nucleotide substitution we successively add 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 publicly available at: http://evogen.molgen.mpg.de/server/substitution-analysis.


Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?


This article has been cited by other articles:


Home page
 Mol Biol EvolHome page
N. D. Singh, P. F. Arndt, A. G. Clark, and C. F. Aquadro
Strong Evidence for Lineage and Sequence Specificity of Substitution Rates and Patterns in Drosophila
Mol. Biol. Evol., July 1, 2009; 26(7): 1591 - 1605.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
W. H. Majoros and U. Ohler
Complexity reduction in context-dependent DNA substitution models
Bioinformatics, January 15, 2009; 25(2): 175 - 182.
[Abstract] [Full Text] [PDF]

Home page
 Mol Biol EvolHome page
F. Squartini and P. F. Arndt
Quantifying the Stationarity and Time Reversibility of the Nucleotide Substitution Process
Mol. Biol. Evol., December 1, 2008; 25(12): 2525 - 2535.
[Abstract] [Full Text] [PDF]

Home page
 Syst BiolHome page
G. Baele, Y. Van de Peer, and S. Vansteelandt
A Model-Based Approach to Study Nearest-Neighbor Influences Reveals Complex Substitution Patterns in Non-coding Sequences
Syst Biol, October 1, 2008; 57(5): 675 - 692.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
M. Peifer, J. E. Karro, and H. H. von Grunberg
Is there an acceleration of the CpG transition rate during the mammalian radiation?
Bioinformatics, October 1, 2008; 24(19): 2157 - 2164.
[Abstract] [Full Text] [PDF]

Home page
 Genome ResHome page
P. Polak and P. F. Arndt
Transcription induces strand-specific mutations at the 5' end of human genes
Genome Res., August 1, 2008; 18(8): 1216 - 1223.
[Abstract] [Full Text] [PDF]

Home page
 Mol Biol EvolHome page
W. Jia and P. G. Higgs
Codon Usage in Mitochondrial Genomes: Distinguishing Context-Dependent Mutation from Translational Selection
Mol. Biol. Evol., February 1, 2008; 25(2): 339 - 351.
[Abstract] [Full Text] [PDF]

Home page
 Mol Biol EvolHome page
C. T. Saunders and P. Green
Insights from Modeling Protein Evolution with Context-Dependent Mutation and Asymmetric Amino Acid Selection
Mol. Biol. Evol., December 1, 2007; 24(12): 2632 - 2647.
[Abstract] [Full Text] [PDF]

Home page
 Proc. Natl. Acad. Sci. USAHome page
A. Tanay, A. H. O'Donnell, M. Damelin, and T. H. Bestor
Hyperconserved CpG domains underlie Polycomb-binding sites
PNAS, March 27, 2007; 104(13): 5521 - 5526.
[Abstract] [Full Text] [PDF]

Home page
 Proc. Natl. Acad. Sci. USAHome page
V. Mustonen and M. Lassig
Evolutionary population genetics of promoters: Predicting binding sites and functional phylogenies
PNAS, November 1, 2005; 102(44): 15936 - 15941.
[Abstract] [Full Text] [PDF]


Disclaimer: Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.