Skip to main content
Article
Better primer design for metagenomics applications by increasing taxonomic distinguishability
HWCOM Faculty Publications
  • Melita Jaric, Bioinformatics Research Group (BioRG), School of Computing and Information Sciences, Florida Intl. Univ., Miami, Florida
  • Jonathan Segal, Department of Molecular Microbiology and Infectious Diseases, Florida International University, Miami, Florida
  • Eugenia Silva-Herzog, Department of Molecular Microbiology and Infectious Diseases, Florida International University, Miami, Florida
  • Lisa Schneper, Department of Molecular Microbiology and Infectious Diseases, Florida International University, Miami, Florida
  • Kalai Mathee, Department of Molecular Microbiology and Infectious Diseases, Florida International University, Miami, Florida
  • Giri Narasimhan, Bioinformatics Research Group (BioRG), School of Computing and Information Sciences, Florida Intl. Univ., Miami, Florida
Date of this Version
12-20-2013
Document Type
Article
Abstract

Current methods of understanding microbiome composition and structure rely on accurately estimating the number of distinct species and their relative abundance. Most of these methods require an efficient PCR whose forward and reverse primers bind well to the same, large number of identifiable species, and produce amplicons that are unique. It is therefore not surprising that currently used universal primers designed many years ago are not as efficient and fail to bind to recently cataloged species. We propose an automated general method of designing PCR primer pairs that abide by primer design rules and uses current sequence database as input. Since the method is automated, primers can be designed for targeted microbial species or updated as species are added or deleted from the database. In silico experiments and laboratory experiments confirm the efficacy of the newly designed primers for metagenomics applications.

Comments
This article was originally published in Biomed Central: BMC Proceedings.
Identifier
FIDC001531
Creative Commons License
Creative Commons Attribution 3.0
Citation Information
Melita Jaric, Jonathan Segal, Eugenia Silva-Herzog, Lisa Schneper, et al.. "Better primer design for metagenomics applications by increasing taxonomic distinguishability" (2013)
Available at: http://works.bepress.com/kalai_mathee/4/