[meltsim] ANNOUNCE: 2.0 beta release!

[J.W. Bizzaro]

Hi Paul,

Monis, Paul wrote:
> Is the Unix port the same as the windows version in terms of the parameters,
> etc used?

The Unix CLI version uses empirical parameters derived by Dick Blake in
1998.  These values were initially placed in the original FORTRAN version of
MeltSim.  The Windows version of MeltSim was developed before 1998 and used
parameters derived by Dick in 1995, as mentioned on the website.

This is the only difference between the Windows and Unix versions in terms of
the melting algorithm used, and it appears that the difference in data produced 
is negligible: I noticed a Tm increase of less than 0.3%.  I've attached a 
graph showing a comparison.

> If not, can the Unix version be compiled to run under linux?

I actually did the translation and porting on a Linux system.  It would be more
accurate for me to say that it is a version for Unix-like command line
interfaces.  And since it is written in ANSI C, you should be able to compile
it on Windows using Cygwin:

   http://www.cygwin.com/

The Windows version also seems to run properly on Linux under Wine:

   http://www.winehq.com/

> I was also wondering if you have ever compared the predictions of meltsim
> with other prediction tools such as the web-based Poland service?

I tried the same sequence once on both MeltSim and the Poland-Service and did
not get a similar derivative profile.  It seems that the Poland-Service makes 
use of several of Dick Blake's developments, but I can't explain the different 
results without a more detailed evaluation.

I've also tried the same sequence on Dan:

   http://bioweb.pasteur.fr/seqanal/interfaces/dan.html

Since Dan produces a positional profile plot (one melting point per base), I
could only make that comparison, but they seemed to identify the same
positional melting characteristics.

I haven't performed any detailed evaluations, however.  These were just quick 
comparisons out of curiousity on my part.

Cheers,
Jeff
-- 
J.W. Bizzaro
Bioinformatics Organization, Inc. (Bioinformatics.Org)
E-mail: jeff at bioinformatics.org
Phone:  +1 508 890 8600
--

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