MPrime: efficient large scale multiple primer and oligonucleotide design for customized gene microarrays.
BACKGROUND
Enhancements in sequencing technology have recently yielded assemblies of large genomes including rat, mouse, human, fruit fly, and zebrafish. 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 primer pairs or oligonucleotides en masse rather than using a time consuming and laborious gene-by-gene method.


RESULTS
We have developed an integrated system, MPrime, in order to efficiently calculate primer pairs or specific oligonucleotides for multiple genic regions based on a keyword, gene name, accession number, or sequence fasta format within the rat, mouse, human, fruit fly, and zebrafish genomes. A set of products created for mouse housekeeping genes from MPrime-designed primer pairs has been validated using both PCR-amplification and DNA sequencing.


CONCLUSIONS
These results indicate MPrime accurately incorporates standard PCR primer design characteristics to produce high scoring primer pairs for genes of interest. In addition, sequence similarity for a set of oligonucleotides constructed for the same set of genes indicates high specificity in oligo design.
Rouchka
Eric C
EC
Department of Computer Engineering and Computer Science, Speed School of Engineering, University of Louisville, Louisville, Kentucky, USA. eric.rouchka@louisville.edu
Khalyfa
Abdelnaby
A
Cooper
Nigel G F
NG
D000818:Animals; D017931:DNA Primers; D030541:Databases, Genetic; D006801:Humans; D016247:Information Storage and Retrieval / Q000379:methods; D020411:Oligonucleotide Array Sequence Analysis / Q000295:instrumentation* / Q000379:methods*; D016133:Polymerase Chain Reaction; D012680:Sensitivity and Specificity; D016415:Sequence Alignment; D012984:Software; D012985:Software Design; D012986:Software Validation; D014584:User-Computer Interface
D017931:DNA Primers