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ePrime: A powerful design engine with simple interface

By Dr. Dale Kunde

Dale is the principle lecturer in Clinical Biochemistry and Molecular Biology within the School of Human Life Sciences. He is member of a team that possess extensive professional experience that are responsible for the Biomedical Science programme.

The explosion of molecular techniques utilising PCR over the recent decades has driven the need for more accurate algorithms and software for design of oligonucleotide primers. Good primer design is imperative for simple PCR, real-time PCR and the newer technologies such as Dual-labelled hydrolysis (Taqman) and Molecular Beacon assays which involve the concomitant design of specific probes for SNP or genetic expression analysis. At the University of Tasmania, we have a significant research programme using real-time qPCR and Taqman probe based assays for the analysis of genetic expression in a range of research projects into Coagulopathies, Inflammatory Bowel Disease and Glaucoma as well as real-time PCR techniques for the identification and differentiation of Haemophilus species.

Polyclone's ePrime application provides a powerful design engine behind a relatively straightforward interface that enables the researcher to design oligonucleotide primers for simple and real-time PCR whilst also designing oligonucleotide probes for more advanced assays. The package allows for simple design using a range of default parameters, such as primer size range, Tm range etc., for the design of primers and probes, which are well defined. However, the scope is available for more complex assays allowing user defined parameters to suit the particular design profile prior to primer design. I particularly liked the mapping algorithm to locate primers within the input sequence. The ability to obtain Genbank sequences directly as well as the ability to run BLAST and secondary structure analysis through NCBI tools is certainly advantageous.