title: TfReg: calculating DNA and RNA melting temperatures and opening profiles with mesoscopic models.
abstract: CONCLUSIONS
  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.
  
  
  BACKGROUND
  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.
  
  
  BACKGROUND
  gweberbh@gmail.com
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors.affiliation: Departamento de Física, Universidade Federal Minas Gerais, Belo Horizonte-MG, 31270-901 Brazil. gweberbh@gmail.com
authors.forename: Gerald
authors.initials: G
authors.lastname: Weber
mesh_terms: D004247:DNA / Q000737:chemistry*; D015894:Genome, Human; D006801:Humans; D006860:Hydrogen Bonding; D008956:Models, Chemical; D015233:Models, Statistical; D009841:Oligonucleotides / Q000737:chemistry; D011381:Programming Languages; D012313:RNA / Q000737:chemistry*; D012984:Software; D013696:Temperature
chemical_list: D009841:Oligonucleotides; D012313:RNA; D004247:DNA