From owner-chemistry@ccl.net Wed Apr 5 09:38:00 2006 From: "Sunil Kumar Panigahi sunil.panigrahi-$-gmail.com" To: CCL Subject: CCL: MeltDNA: A software to predict of DNA duplex stability. Message-Id: <-31425-060405080639-7416-POE+HMywT4oVjPdm1VBwFw++server.ccl.net> X-Original-From: "Sunil Kumar Panigahi" Date: Wed, 5 Apr 2006 08:06:36 -0400 Sent to CCL by: "Sunil Kumar Panigahi" [sunil.panigrahi*_*gmail.com] Dear All, We are releasing the first version of MeltDNA. This can be downloaded from the following link. 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