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Bioinformatics Advance Access published online on February 4, 2005
Bioinformatics, doi:10.1093/bioinformatics/bti304
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© The Author (2005). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oupjournals.org
Received August 24, 2004
Revised January 9, 2005
Accepted January 29, 2005

Applications note

ExPrimer: to design primers from exon-exon junctions

Kuljeet S. Sandhu 1 and Kshitish K. Acharya 1*

1 Institute of Bioinformatics and Applied Biotechnology (IBAB), G-05, Tech Park Mall, ITPL, Whitefield road, Bangalore 560066, INDIA

* To whom correspondence should be addressed.
Kshitish K. Acharya, E-mail: kshitish{at}ibab.ac.in


  Abstract

Summary: ExPrimer is a web based computer program to design primers mainly from a specified exon-exon junction (E-E-jn) of a gene of interest. The tool suggests the optimum primer-pair(s) of which the right (reverse) primer represents a particular E-E-jn of the mRNA. The ‘product length’ decides location of the left primer. The results also include all other primer pairs considered and their ‘scores’. ExPrimer can use the NCBI BLASTn program for sequence specificity of primers. The tool is useful in many areas of molecular biology research that involve hybridization of short sequences with mRNA or cDNA.

Availability: http://exprimer.ibab.ac.in/exprimer_html/exprimer.html.


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