Transition Calculations
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Guide to the SIDD Website

This Web page provides users with access to the SIDD algorithm, which calculates the statistical mechanical equilibrium properties of the strand separation transition in a DNA sequence that is under negative superhelical stress. The details of this analytic method are available in the papers 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 level of stress may be used, or specific values may be specified. The stress level is expressed as the superhelix density. This calculation slows considerably as the level of stress is increased, so it is not recommended to use superhelix densities beyond -0.08.

The output of the program consists of two plots. The first shows the calculated denaturation energy profile for the sequence. Here G(x) is the denaturation energy, the incremental energy needed to force the base pair at position x to be open. Stable states have high values of G(x) while destabilized sites have low values. The output also provides the transition profile, the probability of strand separation of each base pair in the submitted sequence. The values of the parameters used in the calculation and several output parameters also are provided. These include the average number of open base pair, the average number of open regions, the minimum energy, and the run time. The user also has the option to download a file containing the numerical data that is plotted in these profiles.

The SIDD algorithm is described in detail in the following paper:
Benham, C.J. and Bi, C.-P. (2004) The Analysis of Stress-Induced Duplex Destabilization in Long Genomic DNA Sequences, J. Comp. Biol. 11: 519-543.

Papers that present or use results calculated with WebSIDD should cite the following paper:
Bi, C.-P. and Benham, C.J. (2004) WebSIDD: Server for Pre dicting Stress-induced Duplex Destabilized (SIDD) Sites in Superhelical DNA, Bioinformatics 20: 1477-1479.