AutoPrime: online primer design for real-time PCR

AutoPrime allows to rapidly design primers for real-time PCR measurement of eukaryotic expression. Such primers are usually selected so that they will amplify cDNA generated from mRNA but will not yield a product on the genomic DNA. This is achieved by taking advantage of the eukaryotic splicing system for (pre-)mRNA. Either primer pairs are selected so that one of the primers matches the exon-exon border sequence (which of course does not exist in the genomic sequence) or the pair is designed by placing each primer in a different exon so that a genomic product would include a long intronic sequence (and thus will be excluded). AutoPrime provides these capabilities using the Primer3 primer-design software and Ensembl sequence data.

Reference:

AutoPrime: selecting primers for expressed sequences

Gunnar Wrobel, Felix Kokocinski and Peter Lichter

Genome Biology 2004, 5:P11

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Last update 19-Aug-2005, Rating n/a of 0 votes.