title: DePIE: Designing Primers for Protein Interaction Experiments.
abstract: 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.
authors.affiliation: McGill Centre for Bioinformatics, School of Computer Science, McGill University, 3775 University Street, Montreal, QC, Canada H3A 2B4. glu3@unlnotes.unl.edu
authors.forename: Guoqing
authors.initials: G
authors.lastname: Lu
authors.forename: Michael
authors.initials: M
authors.lastname: Hallett
authors.forename: Stephanie
authors.initials: S
authors.lastname: Pollock
authors.forename: David
authors.initials: D
authors.lastname: Thomas
mesh_terms: D017931:DNA Primers / Q000737:chemistry*; D030561:Databases, Nucleic Acid; D030562:Databases, Protein; D020407:Internet; D009691:Nucleic Acid Denaturation; D016133:Polymerase Chain Reaction / Q000379:methods*; D021382:Protein Sorting Signals; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000737:chemistry; D017421:Sequence Analysis / Q000379:methods*; D012984:Software; D020798:Two-Hybrid System Techniques; D014584:User-Computer Interface; D015003:Yeasts / Q000235:genetics
chemical_list: D017931:DNA Primers; D021382:Protein Sorting Signals; D011506:Proteins