About

Authors

POLYMORPH written 2007 by Stephan Ossowski and Joffrey Fitz.
This is a part of the POLYMORPH Project by Stephan Ossowski, Joffrey Fitz, Norman Warthmann, Richard Clark, Korbinian Schneeberger, and Detlef Weigel.

© Copyright 2007 Max Planck Institute for Developmental Biology, Tübingen. http://www.weigelworld.org

Contact

Project Leader: Detlef Weigel
Data related questions: Richard Clark, Stephan Ossowski, Korbinian Schneeberger, Norman Warthmann
Software issues: Stephan Ossowski, Joffrey Fitz

How to cite

If you find this information useful then please cite:

Ossowski S, Fitz J, Warthmann N, Clark RM, Schneeberger K and Weigel D, personal communication

and

Richard M. Clark, Gabriele Schweikert, Christopher Toomajian, Stephan Ossowski, Georg Zeller, Paul Shinn, Norman Warthmann, Tina T. Hu, Glenn Fu, David A. Hinds, Huaming Chen, Kelly A. Frazer, Daniel H. Huson, Bernhard Schölkopf, Magnus Nordborg, Gunnar Rätsch, Joseph R. Ecker, and Detlef Weigel
Common Sequence Polymorphisms Shaping Genetic Diversity in Arabidopsis thaliana.
Science 20 July 2007: 338-342

and

Zeller G, Clark RM, Schneeberger K, Bohlen A, Weigel D and Rätsch G.
Detecting Polymorphic Regions in the Arabidopsis thaliana Genome with Resequencing Microarrays,
Genome Res., published online before print March 6, 2008 as doi: doi:10.1101/gr.070169.107

The ADF Format was introduced by Warthmann N, Fitz J, Weigel D. 2007. If you use the term 'ADF' please cite:

Norman Warthmann, Joffrey Fitz and Detlef Weigel.
MSQT for choosing SNP assays from multiple DNA alignments.
Bioinformatics 2007; doi: 10.1093/bioinformatics/btm428

References

We are using The Multiple SNP Query Tool (MSQT):

Norman Warthmann, Joffrey Fitz and Detlef Weigel.
MSQT for choosing SNP assays from multiple DNA alignments.
Bioinformatics 2007; doi: 10.1093/bioinformatics/btm428

We are using Primer3 for designing PCR primers:

Rozen S, Skaletsky H (2000)
Primer3 on the WWW for general users and for biologist programmers.
In: Krawetz S, Misener S (eds)
Bioinformatics Methods and Protocols: Methods in Molecular Biology. Humana Press, Totowa, NJ, pp 365-386
(PDF online available)

For CAPS marker design we use SNP2CAPS and a customized version available here.

Thomas Thiel, Raja Kota, Ivo Grosse, Nils Stein, and Andreas Graner
SNP2CAPS: a SNP and INDEL analysis tool for CAPS marker development.
Nucleic Acids Research, 2004, Vol. 32, No. 1 e5

The GBrowse Genome Annotation Viewer is used for browsing the genome:

Stein, L.D., Mungall, C., Shu, S., Caudy, M., Mangone, M., Day, A., Nickerson, E., Stajich, J.E., Harris, T.W., Arva, A., et al. (2002)
The generic genome browser: a building block for a model organism system database
Genome Res, . 12, 1599-610

Warranty

THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY APPLICABLE LAW. EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT HOLDERS AND/OR OTHER PARTIES PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE PROGRAM IS WITH YOU. SHOULD THE PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF ALL NECESSARY SERVICING, REPAIR OR CORRECTION.