PRIMER Input Form
A string to identify your
output.
E.g. 50,2 requires primers
to surround the 2 bases at positions 50 and 51. Or mark
the source sequence
with [ and ]: e.g. ...ATCT[CCCC]TCAT.. means that
primers
must flank the central CCCC.
E.g. 401,7 68,3 forbids
selection of primers in the 7 bases starting at 401 and
the 3 bases at 68. Or mark the source
sequence with < and >: e.g.
...ATCT<CCCC>TCAT..
forbids primers in the central CCCC.
General Primer Picking Conditions
|
Tm | Lt: | Gt: | ||
Size | Lt: | Gt: | ||
GC% | Lt: | Gt: |
Self Complementarity | |
3' Self Complementarity | |
#N's | |
Mispriming | |
Sequence Quality | |
End Sequence Quality | |
Position Penalty | |
End Stability |
Objective Function Penalty Weights for Primer Pairs
Hyb Oligo (Internal Oligo) Per-Sequence Inputs
Hyb Oligo Excluded Region: |
Hyb Oligo Size: | Min | Opt | Max |
Hyb Oligo Tm: | Min | Opt | Max |
Hyb Oligo GC% | Min: | Opt: | Max: |
Objective Function Penalty Weights for Hyb Oligos (Internal Oligos)
Copyright Notice and Disclaimer
Copyright (c) 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:
-
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.
-
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.
-
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.
-
The name of the Whitehead Institute may not be used to endorse or promote products derived from this software without specific prior written permission.
Steve Rozen, Helen J. Skaletsky (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.
Acknowledgments
The development of Primer3 and
the Primer3 web site was funded by Howard
Hughes Medical Institute and by the National
Institutes of Health,
National Human Genome Research Institute. under grants
R01-HG00257
(to David C. Page) and P50-HG00098 (to Eric S. Lander).
We gratefully acknowledge the support of Digital Equipment Corporation, which provided the Alphas which were used for much of the development of Primer3, and of Centerline Software, Inc., whose TestCenter memory-error, -leak, and test-coverage checker we use regularly to discover and correct otherwise latent errors in Primer3.
Original design of this
primer-picking
web site by Richard Resnick, who also is an author
of this site's documentation. Primer3's design is heavily based
on earlier implementations of similar programs: Primer 0.5
(Steve
Lincoln, Mark Daly, and Eric S. Lander) and Primer v2
(Richard
Resnick). Lincoln Stein championed the use of
the Boulder-IO format and the idea of making the Primer3 engine
a software component.