From: Michael Neff, RE: dCAPS Finder

Michael Neff mneff at
Fri Mar 22 13:34:43 EST 2002

Dear Arabidopsis News Group readers,

I am writing concerning latest developments in dCAPS Finder. For those of
you that are not familiar with this computer program and technique, see the
following refrence:

Neff MM, Neff JD, Chory J and Pepper AE  (1998) dCAPS, a simple technique
for the genetic analysis of single nucleotide polymorphisms: experimental
applications in Arabidopsis thaliana genetics.  Plant Journal, 14 387-392.

If you are using the dCAPS Finder program and are not on the mailing list,
or if you would like a copy of this free program, contact me via email
(mneff at

My lab is currently writing a web-browser based version of dCAPS Finder that
will be usable by anyone with access to the internet. The format will be
very similar to a BLAST search. We are close to completion and will notify
the Arabidopsis News Group when public access will be available.

As a complement to the dCAPS Finder program, we would also like to develop a
program that can give the researcher an indication as to whether their
mismatched dCAPS primer will work or not. It seems that the best way to do
this is to compare the putative primer sequence (the position and type of
mismatch indicated), with a lists of examples that did work or didn't work.
This program would also be web-browser based. The key to such a program
would be the scope of the list. The larger the example list (for both
successes and failures), the more accurate the program.

Since, we have been providing the dCAPS Finder program for free, we were
hoping that each of the labs that has used this program to develop dCAPS
markers would be willing to share with us as many examples of mismatching
primers that have worked as well as those that have not worked. In each
case, we will need both the primer sequence and the wild type sequence plus
enough sequence 3` of the primer (for both templates) to "see" the generated
restriction-site-based dCAPS marker. Of course we promise to keep all
sequence information confidential (as will the new version of dCAPS Finder).

Thank you very much for you future help with this community service.




Michael M. Neff
Assistant Professor
Department of Biology
Washington University
Campus Box 1137
One Brookings Drive
St. Louis, MO 63130

Phone: 314-935-7915
Fax: 314-935-4432
mneff at



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