News: version 7.0 is now available with new parameters for metal mediated DNA (February 2022)
TfReg implements the calculation of Peyrard-Bishop style Hamiltonians to obtain some physical properties of DNA and RNA duplexes. The method uses the transfer matrix technique for the calculation of the classical partition function. Also, TfReg calculates the regression of experimental versus predicted melting temperatures using the equivalent melting index.
Currently TfReg has parameters for
DNA (for various Na⁺ and Mg2+ buffers)
RNA (various Na+ buffers)
GU mismatches in RNA
Inosine in DNA
Cy3 and Cy5 fluorophores in DNA
DNA/RNA hybrids
All configurations of single, double and triple mismatches in DNA
TNA
LNA at high Na+ buffer
Metal mediated DNA (T-Hg2+T and C-Ag+-C)
Mesoscopic models available:
Original Peyrard-Bishop (PB) model
Anharmonic Peyrard-Bishop-Dauxois model
Joyeux and Buyukdagli model
PB model with solvent term
Approximated 3D model
Peyrard, Cuesta-Lopez and Angelov (PCLA) model
Peyrard, Cuesta-Lopez and James (PCLJ) model
Tapia-Rojo, Mazo, and Falo (TRMF) model
Please have a look at the Documentation for more details about what TfReg can do for you and examples of how to install and run the software.
This software is distributed under the GNU General Public License version 3 (GPLv3) and precompiled binary packages for several Linux distributions, as well as the source code, can be found at the OpenSuse Build Service or from our site.
Download version 7.0 for your Linux system
from our site: Binary packages for various Linux distributions and tar source file
from Suse Build Service: Deb or RPM package (OpenSuse, Fedora, Debian, Ubuntu and others)
from Suse: On Click Install
Please note: only OpenSuse 15.1 was fully tested. If you are running into problems for your distribution please send me an email reporting your problem with as much details as possible.
Installation: please refer to your Linux distribution documentation for installation of rpm or deb packages.
Example installation command for openSuse15.1
zypper addrepo http://download.opensuse.org/repositories/home:drgweber/openSUSE_Leap_15.1/home:drgweber.repo zypper refresh zypper install TfReg
Example installation for Fedora 25
dnf config-manager --add-repo http://download.opensuse.org/repositories/home:drgweber/Fedora_25/home:drgweber.repo dnf install TfReg
If you found this software useful, please let me know by sending an email or by adding a comment below (you may need to sign in to your Google account to add comments). It is of considerable help to show a list of users to funding agencies to guarantee continued financial support for the project.