Nucleic Acids Research, 2003, Vol. 31, No. 13 3755-3757
© 2003 Oxford University Press
DePIE: Designing Primers for Protein Interaction Experiments
1 McGill Centre for Bioinformatics, School of Computer Science, McGill University, 3775 University Street, Montreal, QC, Canada H3A 2B4 2 Department of Biochemistry, McGill University, McIntyre Medical Sciences Building, 3655 Promenade Sir William Osler, Montreal, QC, Canada H3G 1Y6
*To whom correspondence should be addressed at Center for Biotechnology and School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE 68588-0665, USA. Tel: +1 4024724982; Fax: +1 4024723139; Email: glu3{at}unlnotes.unl.edu
Several primer prediction and analysis programs have been developed for diverse applications. However, none of these existing programs can be directly used for the design of primers in protein interaction experiments, since proteins may have transmembrane domains (TMDs) and/or a signal peptide that must be excluded from experiments. Furthermore, it is frequently the case that a short restriction sequences must be added to each primer in order to clone PCR products into a given destination vectors for expression. DePIE, a web-based primer design tool, was developed to address these deficiencies. The program takes as input NCBI protein accession numbers and returns primer information including nucleotide sequences, thermodynamic melting temperature of the nucleotide sequences and the target positions. DePIE is implemented in JAVA, PERL and PHP and has proven to be very efficient in designing primers for our interaction experiments. DePIE services can be accessed at the web site: http://biocore.unl.edu/primer/primerPI.html.
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