title: LAVA: an open-source approach to designing LAMP (loop-mediated isothermal amplification) DNA signatures.
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/.
authors.affiliation: Lawrence Livermore National Laboratory, Livermore, California, USA. clinton.torres@llnl.gov
authors.forename: Clinton
authors.initials: C
authors.lastname: Torres
authors.forename: Elizabeth A
authors.initials: EA
authors.lastname: Vitalis
authors.forename: Brian R
authors.initials: BR
authors.lastname: Baker
authors.forename: Shea N
authors.initials: SN
authors.lastname: Gardner
authors.forename: Marisa W
authors.initials: MW
authors.lastname: Torres
authors.forename: John M
authors.initials: JM
authors.lastname: Dzenitis
mesh_terms: D001483:Base Sequence; D017931:DNA Primers / Q000235:genetics; D021141:Nucleic Acid Amplification Techniques; D012680:Sensitivity and Specificity; D016415:Sequence Alignment / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software
chemical_list: D017931:DNA Primers