Introduction

SUMMARY: 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. AVAILABILITY AND IMPLEMENTATION: The package and additional documentation are freely available at https://bitbucket.org/benhamlab/sist_codes. CONTACT: dzhabinskaya@ucdavis.edu.

Publications

  1. SIST: stress-induced structural transitions in superhelical DNA.
    Cite this
    Zhabinskaya D, Madden S, Benham CJ, 2015-02-01 - Bioinformatics (Oxford, England)

Credits

  1. Dina Zhabinskaya
    Developer

    UC Davis Genome Center and Department of Mathematics, University of California, United States of America

  2. Sally Madden
    Developer

    UC Davis Genome Center and Department of Mathematics, University of California, United States of America

  3. Craig J Benham
    Investigator

    UC Davis Genome Center and Department of Mathematics, University of California, United States of America

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Summary
AccessionBT000385
Tool TypeApplication
Category
PlatformsLinux/Unix
Technologies
User InterfaceTerminal Command Line
Download Count0
Country/RegionUnited States of America
Submitted ByCraig J Benham