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Primer3 is a widely used program for designing PCR primers (PCR =
"Polymerase Chain Reaction"). PCR is an essential and ubiquitous tool
in genetics and molecular biology. Primer3 can also design
hybridization probes and sequencing primers.
Primer3 picks primers for PCR reactions, considering as criteria: o
- oligonucleotide melting temperature, size, GC content, and
primer-dimer possibilities,
- PCR product size,
- positional constraints within the source (template) sequence,
- possibilities for ectopic priming (amplifying the wrong sequence), and
- many other constraints.
All of these criteria are user-specifiable as constraints, and some
are specifiable as terms in an objective function that characterizes
an optimal primer pair.
Whitehead Institute for Biomedical Research provides a basic web-based
front end to primer3 named primer3web at http://fokker.wi.mit.edu/
Wageningen University Laboratory of Bioinformatics provides a enhanced
web-based front end to primer3 named primer3plus at
http://www.bioinformatics.nl/cgi-bin/primer3plus/primer3plus.cgi
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