[Biodevelopers] binding energy calculation

[Patrick McConnell]

Good pointer, but I need some a little more sophisticated than Tm.  Tm is
probably sufficient for short probes, but I am looking for something more
general that I can apply for gene-to-gene interactions.   This would
include things like base stacking, take into account hairpin loops in the
gene match, etc.

-Patrick





Titus Brown <titus at caltech.edu>@bioinformatics.org on 10/06/2003 04:44:08
PM

Please respond to biodevelopers at bioinformatics.org

Sent by:    biodevelopers-admin at bioinformatics.org


To:    biodevelopers at bioinformatics.org
cc:

Subject:    Re: [Biodevelopers] binding energy calculation

-> Does anyone know of a tool to calculate the binding affinity between
-> between a short mRNA probe and a gene?  I am familiar with mfold and the
-> vienna rna package, which perform similar calculations (correct me if I
am
-> wrong here), but they calculate energies for self-binding.

Google for 'melting temperature' or 'annealing' instead.  The first hit
is this:

             http://www.retrogen.com/index/melting_template.htm

cheers,
--titus
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