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The development of the DNA sequencing technology and in particularly the emergence of high-throughput sequencing (HTS) has led to progressive accumulation of huge amounts of raw genome sequence data. For this reason, there is a growing demand for in silico approaches to extract useful information from raw sequence data, process the information using virtual tools and predict experimental results already at the planning stage. One such approach is in silico PCR. The usual goal of in silico PCR is to predict which PCR products are synthesized from one or multiple DNA templates. Other common goals include template sequence location in the genome as well as primer/probe design and analysis, such as prediction of melting temperatures and secondary/tetriary structures including hairpins, G-quadruplexes, self-dimers and cross-dimers in primer pairs.
(Kalendar et al., 2017) FastPCR: An in silico tool for fast primer and probe design and advanced sequence analysis. Genomics.