PUNS: transcriptomic- and genomic-in silico PCR for enhanced primer design

Paul C Boutros; Allan B Okey

doi:10.1093/bioinformatics/bth257

PUNS: transcriptomic- and genomic-in silico PCR for enhanced primer design

Bioinformatics. 2004 Oct 12;20(15):2399-400. doi: 10.1093/bioinformatics/bth257. Epub 2004 Apr 8.

Authors

Paul C Boutros¹, Allan B Okey

Affiliation

¹ Department of Pharmacology, University of Toronto, Medical Sciences Building, 1 King's College Circle, Toronto, Ontario, M5S-1A8 Canada. [email protected]

PMID: 15073008
DOI: 10.1093/bioinformatics/bth257

Abstract

We developed a CGI/Perl-based web server to perform in silico polymerase chain reaction (PCR) on PCR primer sequences. The PUNS (Primer-UniGene Selectivity) server simulates PCR reactions by running BLASTN analysis on user-entered primer pairs against both the transcriptome and the genome to assess primer specificity. PUNS is particularly suited for the identification of highly selective primers for quantitative microarray validation.

Availability: Both system access and source-code are freely available at http://okeylabimac.med.utoronto.ca/PUNS.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Algorithms
Chromosome Mapping / methods*
DNA Primers / chemical synthesis
DNA Primers / genetics*
Oligonucleotide Array Sequence Analysis / methods*
Polymerase Chain Reaction / methods*
Sequence Alignment / methods
Sequence Analysis, DNA / methods*
Software*
Transcription, Genetic / genetics*

Substances

DNA Primers