Nucleosome energy predictor based on DNA sequence.
This software is a port of the python script by van der Heijden et al. with minor bug fixes. This software is written in C++ to enable faster analysis of large numbers of sequences.
To compile the NucEnergy software, navigate to the "Release" directory and use the command make all to build the binary.
Usage instructions: NucEnergy -i [input file] -o [output file] -w [window size (74)] -b [amplitude (0.2)] -p [period (10)]
Default values (in parentheses) are taken from the default optimal values in van der Heijden et al.
The input file should be a tab delimited file with the following fields: chr start stop DNA_sequence.
The output file is a tab delimited file with the following fields: chr start stop Energy(kT).
This algorithm was originally published and written in Python by van der Heijden et al.. It was ported to C++ with minor bug fixes by Rohan Shah (rohanshah@uchicago.edu).
For questions, comments, or issues with the software, please contact Rohan Shah (rohanshah@uchicago.edu) or Alex Ruthenburg (aruthenburg@uchicago.edu).