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University of Louisville Bioinformatics

Bioinformatics Research at the University of Louisville

Project:

Multiple Primer Design

Authors:

Eric C. Rouchka (1,3)
Abdelnaby Khalyfa (2,3)
Nigel G.F. Cooper (2,3)

  1. University of Louisville Department of Computer Engineering and Computer Science.
  2. University of Louisville Department of Anatomical Sciences and Neurobiology.
  3. University of Louisville Department of Bioinformatics Research Group.
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, 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 based on a keyword, gene name, or accession number within the rat, mouse, and human genomes.
Results:
A set of products created for mouse housekeeping genes from MPrime-designed primers has been validated using both PCR-amplification and DNA sequencing. These results indicate MPrime accurately incorporates standard PCR primer design characteristics to produce high scoring primer pairs within the mouse, rat, and human genomes.

Web Site: http://kbrin.a-bldg.louisville.edu/Tools/MPrime/

Supported by NIH NCRR P20 RR16481

Citations:
Rouchka EC, Khalyfa A, Cooper NGF. (2005) MPrime: efficient large scale multiple primer and oligonucleotide design for cutomized gene arrays. BMC Bioinformatics, 6:175. (pdf).


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