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...

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Veröffentlicht in:	Bioinformatics 2004-10, Vol.20 (15), p.2399-2400
Hauptverfasser:	Boutros, Paul C., Okey, Allan B.
Format:	Artikel
Sprache:	eng
Schlagworte:	Algorithms Biological and medical sciences Chromosome Mapping - methods DNA Primers - chemical synthesis DNA Primers - genetics Fundamental and applied biological sciences. Psychology General aspects Mathematics in biology. Statistical analysis. Models. Metrology. Data processing in biology (general aspects) Oligonucleotide Array Sequence Analysis - methods Polymerase Chain Reaction - methods Sequence Alignment - methods Sequence Analysis, DNA - methods Software Transcription, Genetic - genetics
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Beschreibung
Zusammenfassung:	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
ISSN:	1367-4803 1460-2059 1367-4811
DOI:	10.1093/bioinformatics/bth257