Bioinformatics. 2009 Jan 15;25(2):276-8. Epub 2008 Nov 27.

MFEprimer: multiple factor evaluation of the specificity of PCR primers.

Source

Beijing Institute of Radiation Medicine, State Key Laboratory of Proteomics, Beijing, China.

Abstract

SUMMARY: We developed a program named MFEprimer for evaluating the specificity of PCR primers based on multiple factors, including sequence similarity, stability at the 3'-end of the primer, melting temperature, GC content and number of binding sites between the primer and DNA templates. MFEprimer can help the user to select more suitable primers before running either standard or multiplex PCR reactions. The cDNA and genomic DNA databases of 10 widely used species, as well as user custom databases, were used as DNA templates for analyzing primers specificity. Furthermore, we maintained a Primer3Plus server with a modified Primer3Manager for one-stop primer design and specificity checking.

PMID:: 19038987; [PubMed - indexed for MEDLINE]

Free full text

Publication Types, MeSH Terms, Substances

Publication Types

MeSH Terms

Substances

DNA Primers

LinkOut - more resources

Full Text Sources

Supplemental Content

Related citations

MPprimer: a program for reliable multiplex PCR primer design. [BMC Bioinformatics. 2010]
MPprimer: a program for reliable multiplex PCR primer design.
Shen Z, Qu W, Wang W, Lu Y, Wu Y, Li Z, Hang X, Wang X, Zhao D, Zhang C. BMC Bioinformatics. 2010 Mar 18; 11:143. Epub 2010 Mar 18.
MultiPrimer: software for multiplex primer design. [Appl Bioinformatics. 2006]
MultiPrimer: software for multiplex primer design.
Lee C, Wu JS, Shiue YL, Liang HL. Appl Bioinformatics. 2006; 5(2):99-109.
Review Graphical design of primers with PerlPrimer. [Methods Mol Biol. 2007]
Review Graphical design of primers with PerlPrimer.
Marshall O. Methods Mol Biol. 2007; 402:403-14.
AutoDimer: a screening tool for primer-dimer and hairpin structures. [Biotechniques. 2004]
AutoDimer: a screening tool for primer-dimer and hairpin structures.
Vallone PM, Butler JM. Biotechniques. 2004 Aug; 37(2):226-31.
Review Selection for 3'-end triplets for polymerase chain reaction primers. [Methods Mol Biol. 2007]
Review Selection for 3'-end triplets for polymerase chain reaction primers.
Onodera K. Methods Mol Biol. 2007; 402:61-74.

See reviews... See all...

Cited by 7 PubMed Central articles

Highly Parallel and Short-Acting Amplification with Locus-Specific Primers to Detect Single Nucleotide Polymorphisms by the DigiTag2 Assay. [PLoS One. 2012]
Highly Parallel and Short-Acting Amplification with Locus-Specific Primers to Detect Single Nucleotide Polymorphisms by the DigiTag2 Assay.
Nishida N, Mawatari Y, Sageshima M, Tokunaga K. PLoS One. 2012; 7(1):e29967. Epub 2012 Jan 13.
pcrEfficiency: a Web tool for PCR amplification efficiency prediction. [BMC Bioinformatics. 2011]
pcrEfficiency: a Web tool for PCR amplification efficiency prediction.
Mallona I, Weiss J, Egea-Cortines M. BMC Bioinformatics. 2011 Oct 20; 12:404. Epub 2011 Oct 20.
Alternative splicing of the human gene SYBL1 modulates protein domain architecture of Longin VAMP7/TI-VAMP, showing both non-SNARE and synaptobrevin-like isoforms. [BMC Mol Biol. 2011]
Alternative splicing of the human gene SYBL1 modulates protein domain architecture of Longin VAMP7/TI-VAMP, showing both non-SNARE and synaptobrevin-like isoforms.
Vacca M, Albania L, Della Ragione F, Carpi A, Rossi V, Strazzullo M, De Franceschi N, Rossetto O, Filippini F, D'Esposito M. BMC Mol Biol. 2011 May 24; 12:26. Epub 2011 May 24.

See all...

Related information

Related Citations
Calculated set of PubMed citations closely related to the selected article(s) retrieved using a word weight algorithm. Related articles are displayed in ranked order from most to least relevant, with the “linked from” citation displayed first.
Cited in PMC
Full-text articles in the PubMed Central Database that cite the current articles.

Recent activity

Clear Turn Off Turn On

MFEprimer: multiple factor evaluation of the specificity of PCR primers.
MFEprimer: multiple factor evaluation of the specificity of PCR primers.
Bioinformatics. 2009 Jan 15 ;25(2):276-8. Epub 2008 Nov 27 .

PubMed
Hyperhidrosis: evolving therapies for a well-established phenomenon.
Hyperhidrosis: evolving therapies for a well-established phenomenon.
Mayo Clin Proc. 2005 May ;80(5):657-66.

PubMed
Ribosomal S6 kinase signaling and the control of translation.
Ribosomal S6 kinase signaling and the control of translation.
Exp Cell Res. 1999 Nov 25 ;253(1):100-9.

PubMed
The past twenty-five years in eye banking.
The past twenty-five years in eye banking.
Cornea. 2000 Sep ;19(5):754-65.

PubMed
Bilateral fitting of BAHAs and BAHA fitted in unilateral deaf persons: acoustica...
Bilateral fitting of BAHAs and BAHA fitted in unilateral deaf persons: acoustical aspects.
Int J Audiol. 2005 Mar ;44(3):178-89.

PubMed

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

PubMed

Display Settings:

Send to: