Bioinformatic Comparisons of Some Web-based PCR Primer Design Programs

Bioinformatics has become an indispensable tool for both basic and applied research in biotechnology in the life sciences. The polymerase chain reaction (PCR) is a laboratory method that can be used to quickly amplify a large number of identical copies of a specific DNA segment. In PCR, short synthetic DNA fragments known as primers are used to selectively amplify a specific section of the genome. For PCR to be as efficient and specific as possible, it is important to choose an effective primer sequence and use the correct concentration of primers. If the primer is not designed carefully, non-specific amplification and/or primer dimer formation may occur, which may prevent product formation. Currently, a number of different design tools are available on the internet to assist molecular geneticists in designing PCR primers under optimal conditions. In this study, out of 39 web-based PCR primer design programs, 7 accessible, freely available and widely used web-based PCR primer design programs (NCBI, Primer3, Biserach, Genscript and Primer3plus; Stitcher 2.0; and PrimerQest Tool) were compared using bioinformatics applications for genomic sequences. The advantages and disadvantages of the web-based PCR programs are discussed on the basis of the comparison results.