Skip Navigation


Nucleic Acids Research Advance Access originally published online on January 18, 2008
Nucleic Acids Research 2008 36(3):e16; doi:10.1093/nar/gkm1181
This Article
Right arrow Full Text Freely available
Right arrow Print PDF (936K) Freely available
Right arrow Screen PDF (259K) Freely available
Right arrow Supplementary Data
Right arrowOA All Versions of this Article:
36/3/e16    most recent
gkm1181v1
Right arrow Alert me when this article is cited
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 arrow Commercial Re-use Guidelines
for Open Access NAR Content
Google Scholar
Right arrow Articles by Sivaraman, K.
Right arrow Articles by Cole, A. M.
PubMed
Right arrow PubMed Citation
Right arrow Articles by Sivaraman, K.
Right arrow Articles by Cole, A. M.
Related Collections
Right arrow Nucleic acid amplification
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

Nucleic Acids Research, 2008, Vol. 36, No. 3 e16
© 2008 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Methods Online

Codon choice in genes depends on flanking sequence information—implications for theoretical reverse translation

Karthikeyan Sivaraman1, AswinSaiNarain Seshasayee2, Patrick M. Tarwater3 and Alexander M. Cole1,*

1Department of Molecular Biology and Microbiology, Burnett School of Biomedical Sciences, University of Central Florida, Orlando, FL, 32816, USA, 2Genomics and Regulatory Systems Group, EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK and 3Department of Biostatistics, University of Texas School of Public Health, El Paso, TX, 79902, USA

*To whom correspondence should be addressed. Tel: 407 823 3633; 407 823 3635; Email: acole{at}mail.ucf.edu

Received September 26, 2007. Revised December 7, 2007. Accepted December 27, 2007.

Algorithms for theoretical reverse translation have direct applications in degenerate PCR. The conventional practice is to create several degenerate primers each of which variably encode the peptide region of interest. In the current work, for each codon we have analyzed the flanking residues in proteins and determined their influence on codon choice. From this, we created a method for theoretical reverse translation that includes information from flanking residues of the protein in question. Our method, named the neighbor correlation method (NCM) and its enhancement, the consensus-NCM (c-NCM) performed significantly better than the conventional codon-usage statistic method (CSM). Using the methods NCM and c-NCM, we were able to increase the average sequence identity from 77% up to 81%. Furthermore, we revealed a significant increase in coverage, at 80% identity, from < 20% (CSM) to > 75% (c-NCM). The algorithms, their applications and implications are discussed herein.


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




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.