Primer3

Primer3 helps to choose primers for PCR reactions

“Primer3 is a complete rewrite of the original PRIMER program Primer 0.5, written by Steve Lincoln, Mark Daly, and Eric Lander. See DIFFERENCES FROM EARLIER VERSIONS for a discussion of how Primer3 differs from its predecessors, Primer 0.5 and Primer v2.

Primer3 picks primers for PCR reactions, considering as criteria

o oligonucleotide melting temperature, size, GC content, and primer-dimer possibilities, o PCR product size, o positional constraints within the source sequence, and o miscellaneous 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.”

• from the README file

WWW http//www-genome.wi.mit.edu/genome_software/other/primer3.html