Frontiers in Microbiology (Dec 2019)

GLAPD: Whole Genome Based LAMP Primer Design for a Set of Target Genomes

  • Ben Jia,
  • Xueling Li,
  • Wei Liu,
  • Changde Lu,
  • Xiaoting Lu,
  • Liangxiao Ma,
  • Yuan-Yuan Li,
  • Chaochun Wei,
  • Chaochun Wei

DOI
https://doi.org/10.3389/fmicb.2019.02860
Journal volume & issue
Vol. 10

Abstract

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Loop-mediated isothermal amplification (LAMP) technology has been applied in a wide range of fields such as detection of foodborne bacteria and clinical pathogens due to its simplicity and efficiency. However, existing LAMP primer designing systems require a conserved gene or a short genome region as input, and they can’t design group-specific primers. With the growing number of whole genomes available, it is possible to design better primers to target a set of genomes with high specificity based on whole genomes. We present here a whole Genome based LAMP primer designer (GLAPD), a new system to design LAMP primer for a set of target genomes using whole genomes. Candidate single primer regions are identified genome wide and then combined into LAMP primer sets. For a given set of target genomes, only primer sets amplifying them and only these genomes will be output. In order to accelerate the primer designing, a GPU version is provided as well. The effectiveness of primers designed by GLAPD has been assessed for a wide range of foodborne bacteria. GLAPD can be accessed at http://cgm.sjtu.edu.cn/GLAPD/ or https://github.com/jiqingxiaoxi/GLAPD.git. A simple online version is also supplied to help users to learn and test GLAPD: http://cgm.sjtu.edu.cn/GLAPD/online/.

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