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Nucleic Acids Research 2006 34(Web Server issue):W665-W669; doi:10.1093/nar/gkl297
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© The Author 2006. Published by Oxford University Press. All rights reserved
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions@oxfordjournals.org

Article

PrimerStation: a highly specific multiplex genomic PCR primer design server for the human genome

Tomoyuki Yamada1,*, Haruhiko Soma1,2 and Shinichi Morishita1

1 Department of Computational Biology, Graduate School of Frontier Sciences, University of Tokyo 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8562, Japan 2 Life Science Laboratory, Materials Laboratories, Sony Corporation Shinagawa, Tokyo 144-0001, Japan

*To whom correspondence should be addressed. Tel: +81 47 136 3985; Fax: +81 47 136 3977; Email: yamada{at}cb.k.u-tokyo.ac.jp

Received February 14, 2006. Revised March 1, 2006. Accepted April 7, 2006.

PrimerStation (http://ps.cb.k.u-tokyo.ac.jp) is a web service that calculates primer sets guaranteeing high specificity against the entire human genome. To achieve high accuracy, we used the hybridization ratio of primers in liquid solution. Calculating the status of sequence hybridization in terms of the stringent hybridization ratio is computationally costly, and no web service checks the entire human genome and returns a highly specific primer set calculated using a precise physicochemical model. To shorten the response time, we precomputed candidates for specific primers using a massively parallel computer with 100 CPUs (SunFire 15 K) about 3 months in advance. This enables PrimerStation to search and output qualified primers interactively. PrimerStation can select highly specific primers suitable for multiplex PCR by seeking a wider temperature range that minimizes the possibility of cross-reaction. It also allows users to add heuristic rules to the primer design, e.g. the exclusion of single nucleotide polymorphisms (SNPs) in primers, the avoidance of poly(A) and CA-repeats in the PCR products, and the elimination of defective primers using the secondary structure prediction. We performed several tests to verify the PCR amplification of randomly selected primers for ChrX, and we confirmed that the primers amplify specific PCR products perfectly.

The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors.


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