A tool for dynamic exploration of primers : A dissertation submitted in partial fulfilment of the requirements for the Degree of Bachelor of Applied Computing with Honours at Lincoln University

Abstract

A program has been developed to assist scientists in the biological sciences in the selection of primers for the polymerase chain reaction (PCR). Primer3 is a tool that can suggest primers based on requirements. The traditional query process encourages strict criteria be placed on primers to limit the number of primers suggested and to keep them within an ideal range. However, too often these restrictions are too strict and users must reformulate their queries and try again. Furthermore, there is little guidance on how to adjust the query. Now, broad criteria can be submitted to Primer3 and our program will allow the user to refine the criteria. The program differentiates those primers relating to new criteria using filters. The user can interactively adjust the filters on the suggested primers to see the effect. Primers not meeting the filter criteria are retained to help guide the user to adjust the filter. Interactions provided support dynamic exploration of the data set through allowing rapid, iterative, and reversible changes to filter criteria. Detailed information about selected primers is displayed in a text window for visual inspection and to facilitate a final choice. This solution has been developed using the open-source, cross-platform packages Tcl/Tk and VTK.