AutoPrime: Selecting Primers for Expressed Sequences
Gunnar Wrobel, Felix Kokocinski, Peter Lichter
Genome Research  2004  5:P11
Primers designed for expressed sequences should be specific for the mRNA sequence of a gene but not yield a product from its genomic sequence. Already slight contaminations of genomic DNA can lead to incorrect measurements for sensitive methods like realtime PCR (RT-PCR). The software AutoPrime automates the tedious task of generating such primers for RT-PCR experiments by combining the benefits of the ensembl database with the primer3 software. It can be used as a command-line tool using the language perl or as a web-based application.

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