The codes in this repository are for analyzing three types of structural transitions in superhelical DNA molecules of specified base sequences and kilobase lengths. These are strand separation, BZ transitions and cruciform extrusion. More types of transitions may be added as their energetics become known. The statistical mechanical methods and algorithms used in these analyses are described in the papers cited below.
When using these algorithms you must cite the first paper below, and some or all of the others, depending on which types of analyses you perform:
Zhabinskaya, D., Madden, S., & Benham, C. J. (2015). SIST: stress-induced structural transitions in superhelical DNA. Bioinformatics, 31(3), 421-422.
Fye, R. M. and Benham, C. J. (1999), “Exact method for numerically analyzing a model of local denaturation in superhelically stressed DNA”, Phys Rev E, 59, 3408-3426.
Zhabinskaya, D. and Benham, C. J. (2011), “Theoretical Analysis of the Stress Induced BZ Transition in Superhelical DNA”, PLoS Comput Biol, 7, 1-14.
Zhabinskaya, D. and Benham, C. J. (2013), “Competitive superhelical transitions involving cruciform extrusion”, Nucleic Acids Res, 41(21), 9610-9621.
For questions or problems, please contact either Dina Zhabinskaya (dzhabinskaya@ucdavis.edu), Craig Benham (cjbenham@ucdavis.edu), or Sally Madden (sallymadden@gmail.com).