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Bioinformatics Advance Access originally published online on June 28, 2007
Bioinformatics 2007 23(17):2331-2333; doi:10.1093/bioinformatics/btm343
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© The Author 2007. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

QPRIMER: a quick web-based application for designing conserved PCR primers from multigenome alignments

Namshin Kim and Christopher Lee *

Center for Computational Biology, Molecular Biology Institute, Institute for Genomics and Proteomics, Department of Chemistry and Biochemistry, University of California, Los Angeles, 90095-1570, USA

*To whom correspondence should be addressed.


  Abstract

Summary: We have developed a quick web-based application for designing conserved genomic PCR and RT-PCR primers from multigenome alignments targeting specific exons or introns. We used Pygr (The Python Graph Database Framework for Bioinformatics) to query intervals from multigenome alignments, which gives us less than a millisecond access to any intervals of any genome within multigenome alignments. PRIMER3 was used to extract optimal primers from a gene of interest. QPRIMER creates an electronic genomic PCR image from a set of conserved primers as well as summary pages for primer alignments and products. QPRIMER supports human, mouse, rat, chicken, dog, zebrafish and fruit fly.

Availability: http://www.bioinformatics.ucla.edu/QPRIMER/

Contact: leec{at}mbi.ucla.edu

Associate Editor: Keith Crandall

Received on April 11, 2007; revised on April 11, 2007; accepted on June 23, 2007

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