Hybridization Probes

[Steve Thompson]

Hi everyone - In Article <01IN8PXZNDNMB3V0DD at CLUSTER.NIEHS.NIH.GOV>,
STAFFA at niehs.nih.gov ("NICK STAFFA 361-5444 EXT. 410") wrote:

>Does anyone have any experience using GCG to pick out probes for hybridization?
>Prime comes to mind, but my client seems to find it unsatisfactory.

The GCG Prime program is very good - just be careful to advise your client
as to its intricacies.  As another reader pointed out, it is quite dependent
on the exact PCR/hybrid' conditions simulated.  For an example of how I
teach probe design using homology information as a guide see my exercise #5
for the graduate level bioinformatics course that we teach:

http://ribozyme.vadms.wsu.edu/~vadms/classes/bc578/wk5/Exercise_5S.html

The undergraduate survey course also has a primer design component but does
not use homology inference to tailor the design:

http://ribozyme.vadms.wsu.edu/~vadms/classes/bc378/wk7/exercise7.html

                    I hope you find these helpful.  Cheers - Steve

                                Steven M. Thompson
              Consultant in Molecular Genetics and Sequence Analysis
        Visualization, Analysis & Design in the Molecular Sciences (VADMS)
             Washington State University, Pullman, WA 99164-4660, USA
                  AT&Tnet:  (509) 335-3179  FAX:  (509) 335-9688
                    INTERnet:  thompson at ribozyme.vadms.wsu.edu