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LAVA: An Open-Source Approach To Designing LAMP (Loop-Mediated Isothermal Amplification) DNA Signatures

Clinton Torres*, Elizabeth A Vitalis, Brian R Baker, Shea N Gardner, Marisa W Torres and John M Dzenitis

Author Affiliations

Lawrence Livermore National Laboratory, Livermore, California, USA

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BMC Bioinformatics 2011, 12:240  doi:10.1186/1471-2105-12-240

Published: 16 June 2011

Abstract

Background

We developed an extendable open-source Loop-mediated isothermal AMPlification (LAMP) signature design program called LAVA (LAMP Assay Versatile Analysis). LAVA was created in response to limitations of existing LAMP signature programs.

Results

LAVA identifies combinations of six primer regions for basic LAMP signatures, or combinations of eight primer regions for LAMP signatures with loop primers, which can be used as LAMP signatures. The identified primers are conserved among target organism sequences. Primer combinations are optimized based on lengths, melting temperatures, and spacing among primer sites. We compare LAMP signature candidates for Staphylococcus aureus created both by LAVA and by PrimerExplorer. We also include signatures from a sample run targeting all strains of Mycobacterium tuberculosis.

Conclusions

We have designed and demonstrated new software for identifying signature candidates appropriate for LAMP assays. The software is available for download at http://lava-dna.googlecode.com/ webcite.