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Bioinformatics Advance Access originally published online on February 4, 2005
Bioinformatics 2005 21(9):2091-2092; 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{at}oupjournals.org

ExPrimer: to design primers from exon—exon junctions

Kuljeet S. Sandhu and Kshitish K. Acharya *

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

*To whom correspondence should be addressed.

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 the 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

Contact: kshitish{at}ibab.ac.in


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