[meltsim] Re: methylation?

J.W. Bizzaro jeff at bioinformatics.org
Fri Dec 1 12:43:51 EST 2000

"Dr. Christopher Pearson" wrote:
> I was wondering if the Meltism program can account for melting
> differences due to meCpG status.  Methylation of C residues greatly
> increases the melting temperature of DNAs (Ehrlich,M et al., 1975,
> Biochim. biophys. Acta, 395:109-119; Collins,M. & Myers,RM 1987, J. Mol.
> Biol. 198:737-44).  If Meltism does not permit for this variation can it
> be modified?  Are there other programs that may be able to perform such
> an analyses?  Thank you in advance for your assistance on this.

We had a problem with our mailing list which prevented this message from being
posted.  Here is the reply sent by Dr. Blake:

We do not have the thermodynamic parameters for
methylated CG nearest neighbors. I suppose they
could be determined from delta Tm, but we would,
of course have to assume that the cytosine
residues of all CG neighbors were methylated.
No. That is incorrect. They would be specified
when the sequence is read in. Actually this question
is almost trivial, but we would need the enthalpy
and entropy values as a function of ionic strength.
I am very much in the middle of something, so
if you have the time could you look through the
literature. No way am I going to measure them.
I think my apparatus is kaput now anyway. 

J.W. Bizzaro                                           jeff at bioinformatics.org
Director, Bioinformatics.org: The Open Lab     http://bioinformatics.org/~jeff
"All those scientists--they're all alike!  They say they're working for us,
but what they really want is to rule the world!" 
  -- Angry Villager, Young Frankenstein

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