Simulate_PCR for amplicon prediction and annotation from multiplex, degenerate primers and probes.

ABSTRACT:

Background

Pairing up primers to amplify desired targets and avoid undesired cross reactions can be a combinatorial challenge. Effective prediction of specificity and inclusivity from multiplexed primers and TaqMan®/Luminex® probes is a critical step in PCR design.

Results

Code is described to identify all primer and probe combinations from a list of unpaired, unordered candidates that should produce a product. It predicts and extracts all amplicon sequences in a large sequence database from a list of primers and probes, allowing degenerate bases and user-specified levels of primer-target mismatch tolerance. Amplicons hit by TaqMan®/Luminex® probes are indicated, and products may be annotated with gene information from NCBI. Fragment length distributions are calculated to pr

SUBMITTER: Gardner SN 

PROVIDER: S-EPMC4226945 | biostudies-literature | 2014 Jul

REPOSITORIES: biostudies-literature