MRPrimer: a MapReduce-based method for the thorough design of valid and ranked primers for PCR.

ABSTRACT: Primer design is a fundamental technique that is widely used for polymerase chain reaction (PCR). Although many methods have been proposed for primer design, they require a great deal of manual effort to generate feasible and valid primers, including homology tests on off-target sequences using BLAST-like tools. That approach is inconvenient for many target sequences of quantitative PCR (qPCR) due to considering the same stringent and allele-invariant constraints. To address this issue, we propose an entirely new method called MRPrimer that can design all feasible and valid primer pairs existing in a DNA database at once, while simultaneously checking a multitude of filtering constraints and validating primer specificity. Furthermore, MRPrimer suggests the best primer pair for each target

SUBMITTER: Kim H 

PROVIDER: S-EPMC4787749 | biostudies-literature | 2015 Nov

REPOSITORIES: biostudies-literature