FastPCR: An in silico tool for fast primer and probe design and advanced sequence analysis

•In silico tool for fast primer and probe searching.•Fast primer and probe design and advanced sequence analysis.•Virtual PCR.•Heuristic search algorithm for PCR primers and probes.•In silico DNA fingerprinting.

Polymerase chain reaction (PCR) is one of the most important laboratory techniques used in molecular biology, genetics and molecular diagnostics. The success of a PCR-based method largely depends on the correct nucleic acid sequence analysis in silico prior to a wet-bench experiment. Here, we report the development of an online Java-based software for virtual PCR on linear or circular DNA templates and multiple primer or probe search from large or small databases. Primer or probe sensitivity and specificity are predicted by searching a database to find sequences with an optimal number of mismatches, similarity and stability. The software determines primer location, orientation, efficiency of binding and calculates primer melting temperatures for standard and degenerate oligonucleotides. The software is suitable for batch file processing, which is essential for automation when working with large amounts of data. The online Java software is available for download at http://primerdigital.com/tools/pcr.html.Accession numbers for the sequences resulting from this study:EU140956EU177767EU867815EU882730FJ975775-FJ975780HM481419HM481420KC686837-KC686839KM262797