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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.
If you use SIST, please cite the software itself (see CITATION.cff) along with the paper below, which is required for any use of these algorithms:
Zhabinskaya, D., Madden, S., & Benham, C. J. (2015). SIST: stress-induced structural transitions in superhelical DNA. Bioinformatics, 31(3), 421-422.
Additionally, cite whichever of the following apply to the type(s) of transition you analyze:
| Transition type | Reference |
|---|---|
| Strand separation | 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. |
| BZ transition | Zhabinskaya, D. and Benham, C. J. (2011), "Theoretical Analysis of the Stress Induced BZ Transition in Superhelical DNA", PLoS Comput Biol, 7, 1-14. |
| Cruciform extrusion | 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 CCPBIOSIM@stfc.ac.uk.