MPRIME: Efficient Large Scale Multiple Primer Design for Customized Microarrays

Eric Rouchka1, Nigel Cooper2, Abdelnaby Khalyfa, University of Louisville;, University of Louisville

Motivation: Enhancements in sequencing technology have recently yielded assemblies of large genomes including rat, mouse and human. The availability of large-scale genomic and genic sequence data coupled with advances in microarray technology have made it possible to study the expression of large numbers of sequence products under several different conditions in days where traditional molecular biology techniques might have taken months, or even years. Therefore, In order to efficiently study a number of gene products associated with a disease, pathway, or other biological process, it is necessary to be able to design primers en masse rather than using a time consuming and laborious gene-by-gene method. As a result, we have developed an integrated system, MPrime, in order to efficiently calculate primer pairs for multiple genic regions.

Results: Incorporation of standard PCR primer design characteristics into MPrime has allowed us to efficiently create primer pairs for consideration to be included on microarray chips. MPrime’s interface has allowed for the quick design of primers for genes contained within the rat, mouse and human genomes based on either gene name or accession number.