A Guide to Using FASTPCR Software for PCR, In Silico PCR, and Oligonucleotide Analysis

The FastPCR software as an integrated tools environment for PCR primer and probe design and for prediction of oligonucleotide properties. The software provides comprehensive tools for designing primers for most PCR and perspective applications, including standard, multiplex, long-distance, inverse, real-time with TaqMan probe, Xtreme Chain Reaction (XCR), group-specific, overlap-extension PCR for multi-fragment assembling cloning, and isothermal amplification (Loop-mediated Isothermal Amplification). A programme is available to design specific oligonucleotide sets for long sequence assembly by ligase chain reaction and to design multiplexed of overlapping and non-overlapping DNA amplicons that tile across a region(s) of interest for targeted next-generation sequencing, competitive allele specific PCR (KASP) based genotyping assay for single nucleotide polymorphisms and insertions and deletions at specific loci, among other features. The in silico PCR primer or probe search includes comprehensive analyses of individual primers and primer pairs. FastPCR includes various bioinformatics tools for analysis and searching of sequences, restriction I-II-III type enzyme endonuclease analysis and pattern searching. The program also supports the assembly of a set of contiguous sequences, consensus sequence generation, and sequence similarity and conservancy analysis. FastPCR performs efficient and complete detection of various repeat types with visual display. FastPCR allows for sequence file batch processing that is essential for automation. The software is available for download at https://primerdigital.com/fastpcr.html and online version at https://primerdigital.com/tools/pcr.html.