[Bioperl-l] MeltDNA: A software to prediction of DNA duplex stability and thermodynamics.

Sean Davis sdavis2 at mail.nih.gov
Thu Apr 6 06:45:37 EDT 2006


I just looked quickly but did not see a publication describing the methods
in detail or comparison with other methods.  Is such a document available?


On 4/6/06 1:13 AM, "ch01ph14 at uohyd.ernet.in" <ch01ph14 at uohyd.ernet.in>

>                            Announcement
>                            ------------
> Dear All,
> We are releasing the first version of MeltDNA. This can be downloaded from.
> http://meltdna.sourceforge.net
>                       Overview of the software
>                       -------------------------
> Prediction of DNA duplex stability and thermodynamics is invaluable for
> many molecular biology applications involving sequence dependent
> hybridization reactions. Sequence dependent stability of duplex DNA plays
> a major role in fundamental processes of the living cell, such as
> replication, transcription, and recombination. Many techniques in
> molecular biology depend on the oligonucleotide melting temperature (Tm),
> and several formulas have been developed to estimate Tm. We have developed
> a Perl based tool to predict DNA duplex hybridization & melting
> thermo-dynamics.
>   This tool consider all factors those determine thermodynamic values
> like-Base composition,NN parameters, salt dependency (Na+, Mg++),
> internal mismatch, dangling ends ,loops etc. For improve NN(nearest
> neighbour) model based calculations we introduced fusion matrices.
> MeltDNA provides better prediction accuracy for DNA duplex hybridization
> especially its ability to handle the structural features in DNA duplex
> like loops, loop size etc. It has got wide applicability in primer
> selection in PCR, probe selection in Microarrays, DNA secondary
> structure stability prediction, DNA computing etc.
> Comments are always welcome to improve the software quality.
> Best Regards,
> Sunil
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