DePIE

Designing primers for protein interaction experiments

Guoqing Lu, Michael Hallett, Stephanie Pollock, David Thomas

Research output: Contribution to journalArticle

7 Citations (Scopus)

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.

Original languageEnglish (US)
Pages (from-to)3755-3757
Number of pages3
JournalNucleic acids research
Volume31
Issue number13
DOIs
StatePublished - Jul 1 2003

Fingerprint

Proteins
Protein Sorting Signals
Thermodynamics
Freezing
Clone Cells
Polymerase Chain Reaction
Temperature

ASJC Scopus subject areas

  • Genetics

Cite this

DePIE : Designing primers for protein interaction experiments. / Lu, Guoqing; Hallett, Michael; Pollock, Stephanie; Thomas, David.

In: Nucleic acids research, Vol. 31, No. 13, 01.07.2003, p. 3755-3757.

Research output: Contribution to journalArticle

Lu, G, Hallett, M, Pollock, S & Thomas, D 2003, 'DePIE: Designing primers for protein interaction experiments', Nucleic acids research, vol. 31, no. 13, pp. 3755-3757. https://doi.org/10.1093/nar/gkg577
Lu, Guoqing ; Hallett, Michael ; Pollock, Stephanie ; Thomas, David. / DePIE : Designing primers for protein interaction experiments. In: Nucleic acids research. 2003 ; Vol. 31, No. 13. pp. 3755-3757.
@article{dc307e6619284ef6a8c5b3d90a609273,
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.",
author = "Guoqing Lu and Michael Hallett and Stephanie Pollock and David Thomas",
year = "2003",
month = "7",
day = "1",
doi = "10.1093/nar/gkg577",
language = "English (US)",
volume = "31",
pages = "3755--3757",
journal = "Nucleic Acids Research",
issn = "0305-1048",
publisher = "Oxford University Press",
number = "13",

}

TY - JOUR

T1 - DePIE

T2 - Designing primers for protein interaction experiments

AU - Lu, Guoqing

AU - Hallett, Michael

AU - Pollock, Stephanie

AU - Thomas, David

PY - 2003/7/1

Y1 - 2003/7/1

N2 - 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.

AB - 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.

UR - http://www.scopus.com/inward/record.url?scp=0041620207&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=0041620207&partnerID=8YFLogxK

U2 - 10.1093/nar/gkg577

DO - 10.1093/nar/gkg577

M3 - Article

VL - 31

SP - 3755

EP - 3757

JO - Nucleic Acids Research

JF - Nucleic Acids Research

SN - 0305-1048

IS - 13

ER -