TfReg: calculating DNA and RNA melting temperatures and opening profiles with mesoscopic models

Abstract

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. 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. gweberbh@gmail.com Supplementary data are available at Bioinformatics online.