DePIE

DePIE designs PCR primers for protein interaction experiments, excluding transmembrane domains (TMDs) and signal peptides and permitting incorporation of short restriction sequences for cloning into expression vectors.

Key Features:

• Targeted primer design: Designs primers that exclude protein regions such as transmembrane domains (TMDs) and signal peptides to avoid inclusion of those regions in interaction constructs.
• Restriction site incorporation: Allows addition of short restriction sequences to each primer to facilitate cloning of PCR products into specific destination vectors for expression.
• Output details: Accepts NCBI protein accession numbers and reports nucleotide primer sequences, thermodynamic melting temperatures, and precise target positions on the protein sequence.
• Implementation: Implemented using JAVA, PERL, and PHP.

Scientific Applications:

• Protein interaction studies: Generates primers tailored for constructing expression clones used in assays of protein–protein interactions.
• Cloning and expression: Produces primers with restriction sites suitable for cloning PCR products into destination vectors for protein expression experiments.
• Molecular biology and biochemistry workflows: Provides primer sequences and melting temperatures needed for downstream PCR amplification and construct validation.

Methodology:

Accepts NCBI protein accession numbers, identifies and excludes transmembrane domains and signal peptides, incorporates specified short restriction sequences into primers, and outputs nucleotide primer sequences with calculated thermodynamic melting temperatures and target positions.