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• W2171375066 abstract "Abstract Summary: The mesoscopic statistical physics models, known generically as Peyrard–Bishop (PB) models, have found many applications for the study of oligonucleotide properties. Unfortunately, PB models have not reached a wider non-specialized audience for the lack of freely available software implementations. Here we present an extensible C++ implementation of four variants of the PB model, which allows the user to calculate melting temperatures from tested model parameters. Even for a non-specialist, it should be straightforward to change these parameters to reflect different experimental environments or different types of oligonucleotides. For users with some proficiency in C++ programming, it should be feasible to extend the code to other PB models owing to the generic programming implementation adopted for TfReg. Pre-calculated parameters are included that allow the immediate calculation of melting temperatures and thermal equivalence indexes for DNA and RNA. Availability: C++ source code and compiled binaries for several Linux distributions are available from https://sites.google.com/site/geraldweberufmg/tfreg and from OpenSuse build service at http://build.opensuse.org. Contact: gweberbh@gmail.com Supplementary information: Supplementary data are available at Bioinformatics online." @default.
• W2171375066 created "2016-06-24" @default.
• W2171375066 creator A5085726797 @default.
• W2171375066 date "2013-03-16" @default.
• W2171375066 modified "2023-09-27" @default.
• W2171375066 title "TfReg: calculating DNA and RNA melting temperatures and opening profiles with mesoscopic models" @default.
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• W2171375066 doi "https://doi.org/10.1093/bioinformatics/btt133" @default.
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