Better primer design for metagenomics applications by increasing taxonomic distinguishability

BMC Proceedings - Tập 7 - Trang 1-10 - 2013
Melita Jaric1, Jonathan Segal2, Eugenia Silva-Herzog2, Lisa Schneper2, Kalai Mathee2, Giri Narasimhan1
1Bioinformatics Research Group (BioRG), School of Computing and Information Sciences, Florida Intl. Univ, Miami, USA
2Department of Molecular Microbiology and Infectious Diseases, Florida International University, Miami, USA

Tóm tắt

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.

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