CREPE (CREate Primers and Evaluate): A Computational Tool for Large-Scale Primer Design and Specificity Analysis.

ABSTRACT:

Background/objectives

Polymerase chain reaction (PCR) is ubiquitous in biological research labs, as it is a fast, flexible, and cost-effective technique to amplify a DNA region of interest. However, manual primer design can be an error-prone and time-consuming process depending on the number and composition of target sites. While Primer3 has emerged as an accessible tool to solve some of these issues, additional computational pipelines are required for appropriate scaling. Moreover, this does not replace the manual confirmation of primer specificity (i.e., the assessment of off-targets).

Methods

To overcome the challenges of large-scale primer design, we fused the functionality of Primer3 and In-Silico PCR (ISPCR); this integrated pipeline, CREPE (CREate Primers and Evaluate

SUBMITTER: Pitsch JW 

PROVIDER: S-EPMC12469620 | biostudies-literature | 2025 Sep

REPOSITORIES: biostudies-literature