Skip Navigation


Bioinformatics Advance Access first published online on June 28, 2007
This version published online on July 20, 2007
Bioinformatics, doi:10.1093/bioinformatics/btm343
This Article
Right arrow Advance Access manuscript (PDF) Freely available
Right arrow All Versions of this Article:
23/17/2331    most recent
btm343v2
btm343v1
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrowRequest Permissions
Google Scholar
Right arrow Articles by Kim, N.
Right arrow Articles by Lee, C.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Kim, N.
Right arrow Articles by Lee, C.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

© 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. Prof. Christopher Lee, E-mail: leec{at}mbi.ucla.edu


  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: Prof. Keith Crandall

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

Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?


This article has been cited by other articles:


Home page
 Nucleic Acids ResHome page
M. Bekaert and E. C. Teeling
UniPrime: a workflow-based platform for improved universal primer design
Nucleic Acids Res., June 1, 2008; 36(10): e56 - e56.
[Abstract] [Full Text] [PDF]


Disclaimer:
Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.