BiSearch: ePCR tool for native or bisulfite-treated genomic template

Research output: Chapter in Book/Report/Conference proceedingChapter

16 Citations (Scopus)

Abstract

The design of adequate primers for polymerase chain reaction (PCR) is sometimes a difficult task. This is the case when either the target sequence harbors unusual nucleotide motifs or the template is complex. Unusual nucleotide motifs can be repeat elements, whereas complex templates are targets for mispriming and alternative amplification products. Such examples are GC-rich native or bisulfite-treated genomic DNA sequences. Bisulfite treatment leads to the specific conversion of non-methylated cytosines to uracyls. This is the key step of bisulfite genomic sequencing, widely used to determine DNA methylation of a sequence. Here, we describe BiSearch Web server (http://bisearch.enzim.hu), a primer design software created for designing primers to amplify such target sequences. Furthermore, we developed a unique post-design primer analysis module, to carry out genome wide searches to identify genomic mispriming sites and to test by electronic (in silico) PCR (ePCR) for alternative PCR products. This option is currently available on four native or bisulfite-treated mammalian genomes.

Original languageEnglish
Title of host publicationMethods in Molecular Biology
Pages385-402
Number of pages18
Volume402
DOIs
Publication statusPublished - Aug 2 2007

Publication series

NameMethods in Molecular Biology
Volume402
ISSN (Print)10643745

Fingerprint

Nucleotide Motifs
Polymerase Chain Reaction
Genome
Software Design
Cytosine
DNA Methylation
Computer Simulation
hydrogen sulfite

Keywords

  • DNA methylation
  • Epigenetic control
  • Genomic DNA
  • Methylation-specific PCR (MSP)
  • Mispriming
  • Non-specific amplification
  • Primer design
  • Primer validation
  • Sequence alignment

ASJC Scopus subject areas

  • Molecular Biology
  • Genetics

Cite this

Arányi, T., & Tusnády, G. (2007). BiSearch: ePCR tool for native or bisulfite-treated genomic template. In Methods in Molecular Biology (Vol. 402, pp. 385-402). (Methods in Molecular Biology; Vol. 402). https://doi.org/10.1385/1-59745-528-8:385

BiSearch : ePCR tool for native or bisulfite-treated genomic template. / Arányi, T.; Tusnády, G.

Methods in Molecular Biology. Vol. 402 2007. p. 385-402 (Methods in Molecular Biology; Vol. 402).

Research output: Chapter in Book/Report/Conference proceedingChapter

Arányi, T & Tusnády, G 2007, BiSearch: ePCR tool for native or bisulfite-treated genomic template. in Methods in Molecular Biology. vol. 402, Methods in Molecular Biology, vol. 402, pp. 385-402. https://doi.org/10.1385/1-59745-528-8:385
Arányi T, Tusnády G. BiSearch: ePCR tool for native or bisulfite-treated genomic template. In Methods in Molecular Biology. Vol. 402. 2007. p. 385-402. (Methods in Molecular Biology). https://doi.org/10.1385/1-59745-528-8:385
Arányi, T. ; Tusnády, G. / BiSearch : ePCR tool for native or bisulfite-treated genomic template. Methods in Molecular Biology. Vol. 402 2007. pp. 385-402 (Methods in Molecular Biology).
@inbook{ac6ca340b73946cb86a88d2ee003d234,
title = "BiSearch: ePCR tool for native or bisulfite-treated genomic template",
abstract = "The design of adequate primers for polymerase chain reaction (PCR) is sometimes a difficult task. This is the case when either the target sequence harbors unusual nucleotide motifs or the template is complex. Unusual nucleotide motifs can be repeat elements, whereas complex templates are targets for mispriming and alternative amplification products. Such examples are GC-rich native or bisulfite-treated genomic DNA sequences. Bisulfite treatment leads to the specific conversion of non-methylated cytosines to uracyls. This is the key step of bisulfite genomic sequencing, widely used to determine DNA methylation of a sequence. Here, we describe BiSearch Web server (http://bisearch.enzim.hu), a primer design software created for designing primers to amplify such target sequences. Furthermore, we developed a unique post-design primer analysis module, to carry out genome wide searches to identify genomic mispriming sites and to test by electronic (in silico) PCR (ePCR) for alternative PCR products. This option is currently available on four native or bisulfite-treated mammalian genomes.",
keywords = "DNA methylation, Epigenetic control, Genomic DNA, Methylation-specific PCR (MSP), Mispriming, Non-specific amplification, Primer design, Primer validation, Sequence alignment",
author = "T. Ar{\'a}nyi and G. Tusn{\'a}dy",
year = "2007",
month = "8",
day = "2",
doi = "10.1385/1-59745-528-8:385",
language = "English",
isbn = "1597455288",
volume = "402",
series = "Methods in Molecular Biology",
pages = "385--402",
booktitle = "Methods in Molecular Biology",

}

TY - CHAP

T1 - BiSearch

T2 - ePCR tool for native or bisulfite-treated genomic template

AU - Arányi, T.

AU - Tusnády, G.

PY - 2007/8/2

Y1 - 2007/8/2

N2 - The design of adequate primers for polymerase chain reaction (PCR) is sometimes a difficult task. This is the case when either the target sequence harbors unusual nucleotide motifs or the template is complex. Unusual nucleotide motifs can be repeat elements, whereas complex templates are targets for mispriming and alternative amplification products. Such examples are GC-rich native or bisulfite-treated genomic DNA sequences. Bisulfite treatment leads to the specific conversion of non-methylated cytosines to uracyls. This is the key step of bisulfite genomic sequencing, widely used to determine DNA methylation of a sequence. Here, we describe BiSearch Web server (http://bisearch.enzim.hu), a primer design software created for designing primers to amplify such target sequences. Furthermore, we developed a unique post-design primer analysis module, to carry out genome wide searches to identify genomic mispriming sites and to test by electronic (in silico) PCR (ePCR) for alternative PCR products. This option is currently available on four native or bisulfite-treated mammalian genomes.

AB - The design of adequate primers for polymerase chain reaction (PCR) is sometimes a difficult task. This is the case when either the target sequence harbors unusual nucleotide motifs or the template is complex. Unusual nucleotide motifs can be repeat elements, whereas complex templates are targets for mispriming and alternative amplification products. Such examples are GC-rich native or bisulfite-treated genomic DNA sequences. Bisulfite treatment leads to the specific conversion of non-methylated cytosines to uracyls. This is the key step of bisulfite genomic sequencing, widely used to determine DNA methylation of a sequence. Here, we describe BiSearch Web server (http://bisearch.enzim.hu), a primer design software created for designing primers to amplify such target sequences. Furthermore, we developed a unique post-design primer analysis module, to carry out genome wide searches to identify genomic mispriming sites and to test by electronic (in silico) PCR (ePCR) for alternative PCR products. This option is currently available on four native or bisulfite-treated mammalian genomes.

KW - DNA methylation

KW - Epigenetic control

KW - Genomic DNA

KW - Methylation-specific PCR (MSP)

KW - Mispriming

KW - Non-specific amplification

KW - Primer design

KW - Primer validation

KW - Sequence alignment

UR - http://www.scopus.com/inward/record.url?scp=36049043696&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=36049043696&partnerID=8YFLogxK

U2 - 10.1385/1-59745-528-8:385

DO - 10.1385/1-59745-528-8:385

M3 - Chapter

C2 - 17951807

AN - SCOPUS:36049043696

SN - 1597455288

SN - 9781597455282

VL - 402

T3 - Methods in Molecular Biology

SP - 385

EP - 402

BT - Methods in Molecular Biology

ER -