In silico PCR analysis: a comprehensive bioinformatics tool for enhancing nucleic acid amplification assays

• Published in: Frontiers in Bioinformatics
• Main Authors: Ruslan Kalendar, Alexandr Shevtsov, Zhenis Otarbay, Aisulu Ismailova
• Format: Article
• Language: English
• Published: Frontiers Media S.A. 2024-10-01
• Subjects: In silico PCR; genotyping; PCR primer and probe analysis; degenerate PCR; bisulfite conversion
• Online Access: https://www.frontiersin.org/articles/10.3389/fbinf.2024.1464197/full

Nucleic acid amplification assays represent a pivotal category of methodologies for targeted sequence detection within contemporary biological research, boasting diverse utility in diagnostics, identification, and DNA sequencing. The foundational principles of these assays have been extrapolated to various simple and intricate nucleic acid amplification technologies. Concurrently, a burgeoning trend toward computational or virtual methodologies is exemplified by in silico PCR analysis. In silico PCR analysis is a valuable and productive adjunctive approach for ensuring primer or probe specificity across a broad spectrum of PCR applications encompassing gene discovery through homology analysis, molecular diagnostics, DNA profiling, and repeat sequence identification. The prediction of primer and probe sensitivity and specificity necessitates thorough database searches, accounting for an optimal balance of mismatch tolerance, sequence similarity, and thermal stability. This software facilitates in silico PCR analyses of both linear and circular DNA templates, including bisulfited treatment DNA, enabling multiple primer or probe searches within databases of varying scales alongside advanced search functionalities. This tool is suitable for processing batch files and is essential for automation when working with large amounts of data.