Nucleic Acids Research Advance Access originally published online on April 8, 2008
Nucleic Acids Research 2008 36(9):3095-3100; doi:10.1093/nar/gkn165
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Nucleic Acids Research, 2008, Vol. 36, No. 9 3095-3100
© 2008 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.
Computational Biology |
MultiPriDe: automated batch development of quantitative real-time PCR primers
1Department of Ophthalmology, Emory University, B5500 Clinic B, 1365 Clifton Road NE, Atlanta, GA 30322, USA and 2Department of Biological Sciences, University of Alberta, CW405 Biological Sciences Centre, Edmonton, Alberta T6G 2E9, Canada
*To whom correspondence should be addressed. Tel: +1 404 778 5531; Fax: +1 404 778 4411; Email: aziesel{at}emory.edu
Received January 1, 2008. Revised March 21, 2008. Accepted March 24, 2008.
Quantitative reverse transcriptase polymerase chain reaction (qRT–PCR) is a commonly employed gene expression quantification technique. This requires the development of appropriately targeted oligonucleotide primers, which necessitates the identification of ideal amplicons, development of optimized oligonucleotide sequences under most favorable pre-determined reaction conditions, and management of the resultant target-oligonucleotide pair information for each gene to be studied. The Primer3 utility exists for development of oligonucleotide primers and fills that role effectively. However, the manual process of identifying target sites and individually generating primers is inefficient and prone to user-introduced error, especially when a large number of genes are to be examined. We have developed MultiPriDe (Multiple Primer Design), a Perl utility that accepts batch lists of Gene database identifiers, collects available intron and exon position data critical to qRT–PCR primer development, and supplies these sites as identified targets for the Primer3 utility. This automated ‘gene to primer’ procedure is coupled with a set of optimized hybridization conditions used by the Primer3 utility to maximize successful primer design. MultiPriDe and assembled repeat libraries are available upon request. Please direct requests to aziesel{at}emory.edu.
The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors