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

ch01ph14 at uohyd.ernet.in ch01ph14 at uohyd.ernet.in
Thu Apr 6 01:13:02 EDT 2006

Dear All,

We are releasing the first version of MeltDNA. This can be downloaded from.


                      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
  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,

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