DegePrime, a program for degenerate primer design for broad-taxonomic-range PCR in microbial ecology studies.

ABSTRACT: The taxonomic composition of a microbial community can be deduced by analyzing its rRNA gene content by, e.g., high-throughput DNA sequencing or DNA chips. Such methods typically are based on PCR amplification of rRNA gene sequences using broad-taxonomic-range PCR primers. In these analyses, the use of optimal primers is crucial for achieving an unbiased representation of community composition. Here, we present the computer program DegePrime that, for each position of a multiple sequence alignment, finds a degenerate oligomer of as high coverage as possible and outputs its coverage among taxonomic divisions. We show that our novel heuristic, which we call weighted randomized combination, performs better than previously described algorithms for solving the maximum coverage degenerate primer

SUBMITTER: Hugerth LW 

PROVIDER: S-EPMC4135748 | biostudies-literature | 2014 Aug

REPOSITORIES: biostudies-literature