Skip Navigation

Nucleic Acids Research 2005 33(1):e9; doi:10.1093/nar/gni012
This Article
Right arrow Full Text Freely available
Right arrow Print PDF (194K) Freely available
Right arrow Screen PDF (114K) Freely available
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 Tusnády, Gáb. E.
Right arrow Articles by Arányi, T.ás
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Tusnády, Gáb. E.
Right arrow Articles by Arányi, T.ás
Related Collections
Right arrow Computational methods
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

Published online 13 January 2005

© 2005, the authors Nucleic Acids Research, Vol. 33 No. 1 © Oxford University Press 2005; all rights reserved
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use permissions, please contact journals.permissions{at}oupjournals.org.

Methods Online

BiSearch: primer-design and search tool for PCR on bisulfite-treated genomes

Gábor E. Tusnády, István Simon, András Váradi and Tamás Arányi*

Institute of Enzymology, BRC, Hungarian Academy of Sciences H-1113 Budapest, Karolina út 29, Hungary

*To whom correspondence should be addressed. Tel: +36 1 279 3149; Fax: +36 1 466 5465; Email: aranyi{at}enzim.hu

Received November 22, 2004. Revised December 21, 2004. Accepted December 21, 2004.

Bisulfite genomic sequencing is the most widely used technique to analyze the 5-methylation of cytosines, the prevalent covalent DNA modification in mammals. The process is based on the selective transformation of unmethylated cytosines to uridines. Then, the investigated genomic regions are PCR amplified, subcloned and sequenced. During sequencing, the initially unmethylated cytosines are detected as thymines. The efficacy of bisulfite PCR is generally low; mispriming and non-specific amplification often occurs due to the T richness of the target sequences. In order to ameliorate the efficiency of PCR, we developed a new primer-design software called BiSearch, available on the World Wide Web. It has the unique property of analyzing the primer pairs for mispriming sites on the bisulfite-treated genome and determines potential non-specific amplification products with a new search algorithm. The options of primer-design and analysis for mispriming sites can be used sequentially or separately, both on bisulfite-treated and untreated sequences. In silico and in vitro tests of the software suggest that new PCR strategies may increase the efficiency of the amplification.


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
 BioinformaticsHome page
G. P. Srivastava, J. Guo, H. Shi, and D. Xu
PRIMEGENS-v2: genome-wide primer design for analyzing DNA methylation patterns of CpG islands
Bioinformatics, September 1, 2008; 24(17): 1837 - 1842.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
J. D. Gans and M. Wolinsky
Improved assay-dependent searching of nucleic acid sequence databases
Nucleic Acids Res., July 1, 2008; 36(12): e74 - e74.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
I. M. Carr, E. M. A. Valleley, S. F. Cordery, A. F. Markham, and D. T. Bonthron
Sequence analysis and editing for bisulphite genomic sequencing projects
Nucleic Acids Res., May 21, 2007; (2007) gkm330v1.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
R. M. Brena, H. Auer, K. Kornacker, B. Hackanson, A. Raval, J. C. Byrd, and C. Plass
Accurate quantification of DNA methylation using combined bisulfite restriction analysis coupled with the Agilent 2100 Bioanalyzer platform
Nucleic Acids Res., February 7, 2006; 34(3): e17 - e17.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
C. Bock, S. Reither, T. Mikeska, M. Paulsen, J. Walter, and T. Lengauer
BiQ Analyzer: visualization and quality control for DNA methylation data from bisulfite sequencing
Bioinformatics, November 1, 2005; 21(21): 4067 - 4068.
[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.