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


BACKGROUND
Both system access and source-code are freely available at http://okeylabimac.med.utoronto.ca/PUNS.
Boutros
Paul C
PC
Department of Pharmacology, University of Toronto, Medical Sciences Building, 1 King's College Circle, Toronto, Ontario, M5S-1A8 Canada. Paul.Boutros@utoronto.ca
Okey
Allan B
AB
D000465:Algorithms; D002874:Chromosome Mapping / Q000379:methods*; D017931:DNA Primers / Q000138:chemical synthesis / Q000235:genetics*; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D016133:Polymerase Chain Reaction / Q000379:methods*; D016415:Sequence Alignment / Q000379:methods; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software; D014158:Transcription, Genetic / Q000235:genetics*
D017931:DNA Primers