Transition Calculations
About Dr. Benham
Guide to the SIBZ Website

This Web page provides users with access to the SIBZ algorithm, which calculates the statistical mechanical equilibrium properties of the B-form to Z-form transition in a DNA sequence that is under negative superhelical stress. The details of this analytic method are available in the paper cited below.

Each sequence to be analyzed should not exceed 10,000 bp, with lengths around 5,000 bp being optimal. The sequence can be either in FASTA format or in a file that contains nothing but the A, C, G, and T characters that comprise it. The user must specify whether the sequence is linear or circular. The default temperature and stress level may be used, or specific values may be specified. The stress level is expressed as the superhelix density, which should not exceed -0.07 due to the limitations on the number of Z-forming stretches.

The output of the program consists of two plots of the probability of transition for each base pair in the sequence, also called the transition profile. The values of the parameters used in the calculation and several output parameters also are given. These include the average number of Z-transformed base pair, the average number of Z-DNA runs, minimum energy, and run time. The user also has the option to download a file containing the numerical data shown in transition profiles.

Papers that present or use results calculated with this SIBZ algorithm should cite the following paper:
Zhabinskaya, D and Benham, C.J. (2010) Theoretical Analysis of the Stress Induced B-Z Transition in Superhelical DNA, manuscript in revision.