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

Gyan P. Srivastava, Juyuan Guo, Huidong Shi, Dong Xu

Research output: Contribution to journalArticle

15 Citations (Scopus)

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.

Original languageEnglish (US)
Pages (from-to)1837-1842
Number of pages6
JournalBioinformatics
Volume24
Issue number17
DOIs
StatePublished - Sep 1 2008
Externally publishedYes

Fingerprint

CpG Islands
DNA Methylation
Genetic Promoter Regions
Genome
Genes
DNA sequences
Software design
Promoter
Computer programming languages
Sequencing
Throughput
Programming Languages
Software Design
Biological Phenomena
DNA Sequence
Computer Simulation
High Throughput
Genomics
Cancer
Experiments

ASJC Scopus subject areas

  • Statistics and Probability
  • Biochemistry
  • Molecular Biology
  • Computer Science Applications
  • Computational Theory and Mathematics
  • Computational Mathematics

Cite this

PRIMEGENS-v2 : Genome-wide primer design for analyzing DNA methylation patterns of CpG islands. / Srivastava, Gyan P.; Guo, Juyuan; Shi, Huidong; Xu, Dong.

In: Bioinformatics, Vol. 24, No. 17, 01.09.2008, p. 1837-1842.

Research output: Contribution to journalArticle

Srivastava, Gyan P. ; Guo, Juyuan ; Shi, Huidong ; Xu, Dong. / PRIMEGENS-v2 : Genome-wide primer design for analyzing DNA methylation patterns of CpG islands. In: Bioinformatics. 2008 ; Vol. 24, No. 17. pp. 1837-1842.
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