title: SIST: stress-induced structural transitions in superhelical DNA.
abstract: CONCLUSIONS
  Supercoiling imposes stress on a DNA molecule that can drive susceptible sequences into alternative non-B form structures. This phenomenon occurs frequently in vivo and has been implicated in biological processes, such as replication, transcription, recombination and translocation. SIST is a software package that analyzes sequence-dependent structural transitions in kilobase length superhelical DNA molecules. The numerical algorithms in SIST are based on a statistical mechanical model that calculates the equilibrium probability of transition for each base pair in the domain. They are extensions of the original stress-induced duplex destabilization (SIDD) method, which analyzes stress-driven DNA strand separation. SIST also includes algorithms to analyze B-Z transitions and cruciform extrusion. The SIST pipeline has an option to use the DZCBtrans algorithm, which analyzes the competition among these three transitions within a superhelical domain.
  
  
  METHODS
  The package and additional documentation are freely available at https://bitbucket.org/benhamlab/sist_codes.
  
  
  BACKGROUND
  dzhabinskaya@ucdavis.edu.
authors.affiliation: UC Davis Genome Center and Department of Mathematics, University of California, Davis, CA 95616, USA.
authors.forename: Dina
authors.initials: D
authors.lastname: Zhabinskaya
authors.affiliation: UC Davis Genome Center and Department of Mathematics, University of California, Davis, CA 95616, USA.
authors.forename: Sally
authors.initials: S
authors.lastname: Madden
authors.affiliation: UC Davis Genome Center and Department of Mathematics, University of California, Davis, CA 95616, USA.
authors.forename: Craig J
authors.initials: CJ
authors.lastname: Benham
mesh_terms: D000465:Algorithms; D004278:DNA, Superhelical / Q000737:chemistry*; D006801:Humans; D015233:Models, Statistical; D009690:Nucleic Acid Conformation; D018384:Oxidative Stress / Q000235:genetics*; D012984:Software; D013329:Structure-Activity Relationship
chemical_list: D004278:DNA, Superhelical