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Bioinformatics Advance Access originally published online on June 25, 2008
Bioinformatics 2008 24(17):1837-1842; doi:10.1093/bioinformatics/btn320
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© The Author 2008. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

PRIMEGENS-v2: genome-wide primer design for analyzing DNA methylation patterns of CpG islands

Gyan P. Srivastava 1, Juyuan Guo 2, Huidong Shi 2 and Dong Xu 1,*

1Computer Science Department and Christopher S. Bond Life Sciences Center and 2Department of Pathology and Anatomical Sciences, University of Missouri, Columbia, MO, USA

*To whom correspondence should be addressed.


  Abstract

Motivation: DNA methylation plays important roles in biological processes and human diseases, especially cancers. High-throughput bisulfite genomic sequencing based on new generation of sequencers, such as the 454-sequencing system provides an efficient method for analyzing DNA methylation patterns. The successful implementation of this approach depends on the use of primer design software capable of performing genome-wide scan for optimal primers from in silico bisulfite-treated genome sequences. We have developed a method, which fulfills this requirement and conduct primer design for sequences including regions of given promoter CpG islands.

Results: The developed method has been implemented using the C and JAVA programming languages. The primer design results were tested in the PCR experiments of 96 selected human DNA sequences containing CpG islands in the promoter regions. The results indicate that this method is efficient and reliable for designing sequence-specific primers.

Availability: The sequence-specific primer design for DNA meth-ylated sequences including CpG islands has been integrated into the second version of PRIMEGENS as one of the primer design features. The software is freely available for academic use at http://digbio.missouri.edu/primegens/.

Contact: xudong{at}missouri.edu

Associate Editor: John Quackenbush

Received on December 23, 2007; revised on May 14, 2008; accepted on June 18, 2008

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