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Nucleic Acids Research Advance Access originally published online on May 30, 2007
Nucleic Acids Research 2007 35(Web Server issue):W63-W65; doi:10.1093/nar/gkm383
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Nucleic Acids Research, 2007, Vol. 35, No. suppl_2 W63-W65
© 2007 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Articles

PrimerZ: streamlined primer design for promoters, exons and human SNPs

Ming-Fang Tsai1, Yi-Jung Lin1, Yu-Chang Cheng1, Kuo-Hsi Lee1, Cheng-Chih Huang2, Yuan-Tsong Chen1,2 and Adam Yao1,2,*

1National Genotyping Center (NGC), Academia Sinica, Taipei, Taiwan 11529, R.O.C. and 2Institute of Biomedical Sciences (IBMS), Academia Sinica, Taipei, Taiwan 11529, R.O.C.

*To whom correspondence should be addressed. Tel: +886 2 26523091; Fax: +886 2 27824066; Email: adam{at}ibms.sinica.edu.tw

Received January 31, 2007. Revised April 27, 2007. Accepted April 30, 2007.

PrimerZ (http://genepipe.ngc.sinica.edu.tw/primerz/) is a web application dedicated primarily to primer design for genes and human SNPs. PrimerZ accepts genes by gene name or Ensembl accession code, and SNPs by dbSNP rs or AFFY_Probe IDs. The promoter and exon sequence information of all gene transcripts fetched from the Ensembl database (http://www.ensembl.org) are processed before being passed on to Primer3 (http://frodo.wi.mit.edu/cgi-bin/primer3/primer3_www.cgi) for individual primer design. All results returned from Primer 3 are organized and integrated in a specially designed web page for easy browsing. Besides the web page presentation, csv text file export is also provided for enhanced user convenience.

PrimerZ automates highly standard but tedious gene primer design to improve the success rate of PCR experiments. More than 2000 primers have been designed with PrimerZ at our institute since 2004 and the success rate is over 70%. The addition of several new features has made PrimerZ even more useful to the research community in facilitating primer design for promoters, exons and SNPs.


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