[meltsim] problem running MELSTIM

[richard blake]

Kevin,
Your goal is an interesting one. Good luck. Hopefully you will have  
suitable sensitivity. Years ago I examined the difference in  
stability of poly(dA.dT) and poly(dA.dU), and found the former to be  
significantly more stable than the latter, so methyl groups do affect  
stability. dick blake
On Aug 21, 2007, at 10:52 AM, Marx, Kenneth wrote:

> Hi Kevin,
>
> I don't know how you plan to do the study, but MELTSIM is not
> parameterized for melting methylated bases. This is something that  
> Prof.
> Richard Blake, who developed and parameterized MELTSIM did not do. I
> asked him years ago about this issue of melting methylated bases.
>
> Good luck, Prof. Ken Marx
>
> -----Original Message-----
> From: meltsim-bounces+kenneth_marx=uml.edu at bioinformatics.org
> [mailto:meltsim-bounces+kenneth_marx=uml.edu at bioinformatics.org] On
> Behalf Of Kevin Hollevoet
> Sent: Wednesday, August 15, 2007 12:10 PM
> To: meltsim at bioinformatics.org
> Subject: [meltsim] problem running MELSTIM
>
> hello,
>
> i'm kevin hollevoet, thesisstudent at the university of Ghent
> (belgium) at the medical research building. we are planning to use
> meltsim to preform some large scale simulations to test the
> sensitivity of HRM towards single CpG's methylation differences in NB
> cell lines.
>
> but the problems we are facing are the same like Marko Pavlekovic
> wrote to you some time ago (for the record: i'm using window XP to run
> MELTSIM)
>
> so i tried, just like marko, to change all '.' into ','. even in the
> output files,  when i only selected the meltcurse, the graph was not
> what i would expect. other options they gave also errors for the use
> of E09 (meaning 10^9) in the output file. and that fault (i dont even
> know what the fault is) is obviously not that easy to change in an
> output file.
>
> so is there already some other version on the market or the web?
> perhaps this is some european problem with the configuration of the
> windows XP here? as there are a lot of articles citing your program,
> even recently, it should work somehow perfectly well, no?
>
> greetings
>
> kevin
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