Table of Contents
ISRN Bioinformatics
Volume 2012 (2012), Article ID 696758, 5 pages
http://dx.doi.org/10.5402/2012/696758
Research Article

Electric LAMP: Virtual Loop-Mediated Isothermal AMPlification

1Cullman Program for Molecular Systematics, The New York Botanical Garden, Bronx, NY 10458, USA
2The Graduate Center, The City University of New York, New York, NY 10016, USA

Received 23 August 2012; Accepted 20 September 2012

Academic Editors: D. A. McClellan and F. Pappalardo

Copyright © 2012 Nelson R. Salinas and Damon P. Little. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Abstract

We present eLAMP, a PERL script, with Tk graphical interface, that electronically simulates Loop-mediated AMPlification (LAMP) allowing users to efficiently test putative LAMP primers on a set of target sequences. eLAMP can match primers to templates using either exact (via builtin PERL regular expressions) or approximate matching (via the tre-agrep library). Performance was tested on 40 whole genome sequences of Staphylococcus. eLAMP correctly predicted that the two tested primer sets would amplify from S. aureus genomes and not amplify from other Staphylococcus species. Open source (GNU Public License) PERL scripts are available for download from the New York Botanical Garden's website.