An Interactive Visualisation for Selecting PCR Primers

Rutherford, P., Churcher, C. and McCallum, J.

Biological scientists often need to design primers. These are short pieces of DNA used for copying sections of a DNA sequence using the polymerase chain reaction (PCR). Primers have various properties that influence the likelihood of success and scientists wish to quickly and easily select the best primers for amplification of a target sequence. Current web-based primer design software (Primer3) requires the user to specify ranges for the primer properties and then generates and returns suitable primers. Depending on the range of the criteria this can often result in no suitable primers being found or too many for easy scrutiny. The only option for the user is to adjust the criteria, resubmit the query and hope this will result in manageable number of suitable primers being returned. In this paper we describe a visualisation tool that allows the user to interactively explore the primers suggested by Primer3. The user can soften the criteria ranges submitted to Primer3 to ensure a result and then experiment with adjusting the criteria in order to quickly find the most suitable primers. Initial user trials indicate that the prototype tool is successful in facilitating the choice of suitable primers for a given sequence.

Cite as: Rutherford, P., Churcher, C. and McCallum, J. (2005). An Interactive Visualisation for Selecting PCR Primers. In Proc. Asia Pacific Symposium on Information Visualisation (APVIS2005), Sydney, Australia. CRPIT, 45. Hong, S.-H., Ed. ACS. 21-26.

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