IDT's PrimerQuest © Copyright 2002.

IDT's PrimerQuest incorporates Primer3 software developed by the Whitehead Institute for Biomedical Research, Copyright 1996, 1997. All rights reserved. IDT's PrimerQuest is not identical to Primer3 software distributed by the Whitehead Institute, which in no way endorses IDT's PrimerQuest.

With respect to the use of both IDT's PrimerQuest and Primer3 software, the following conditions apply:

THIS SOFTWARE IS PROVIDED FOR USE IN RESEARCH APPLICATIONS "AS IS", AND ALL EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL IDT OR THE WHITEHEAD INSTITUTE BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

primer3 release 0.9 (distribution 0_9_test)

Copyright © 1996,1997,1998
Whitehead Institute for Biomedical Research. All rights reserved.

Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:

1. Redistributions must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. Redistributions of source code must also reproduce this information in the source code itself.

2. If the program is modified, redistributions must include a notice (in the same places as above) indicating that the redistributed program is not identical to the version distributed by Whitehead Institute.

3. All advertising materials mentioning features or use of this software must display the following acknowledgment: This product includes software developed by the Whitehead Institute for Biomedical Research.

4. The name of the Whitehead Institute may not be used to endorse or promote products derived from this software without specific prior written permission.

We also request that use of this software be cited in publications as

Steve Rozen, Helen J. Skaletsky (1996,1997,1998)
Primer3. Code available at
http://www-genome.wi.mit.edu/genome_software/other/primer3.html

THIS SOFTWARE IS PROVIDED BY THE WHITEHEAD INSTITUTE ''AS IS'' AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE WHITEHEAD INSTITUTE BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

INTRODUCTION
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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:

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

The Whitehead/MIT Center for Genome Research offers web-based front end to Primer3 at http://www.genome.wi.mit.edu/cgi-bin/primer/primer3.cgi.