[BiO BB] state-of-art method for computing Tm for microarray probes, and a probe selection question

[Joe Landman]

Ann Loraine wrote:
> Hello all,
> 
> This is a question for microarray probe designers on the list.
> 
> What in your opinion is the state-of-the-art method for calculating Tm for
> oligos bound to solid substrate?

Hi Ann:

   Not sure if you are aware of these folks, but VisualOMP is supposed 
to be pretty good 
(http://www.dnasoftware.com/Products/VisualOMP/index.htm ).

   I/we don't have anything to do with this company, though I know the 
people who founded it.

> 
> A related question: if you have a 1000 bp target and need to pick some
> number N of probes within that region, how would you do it?
> 
> (Assuming let's say a 66+-2oC hybe temperature.)
> 
> Very best wishes,
> 
> Ann Loraine


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Joseph Landman, Ph.D
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