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Bioinformatics Advance Access published online on May 6, 2004
Bioinformatics, doi:10.1093/bioinformatics/bth304
Bioinformatics © Oxford University Press 2004; all rights reserved
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Received May 8, 2003
Revised June 11, 2003
Accepted July 29, 2003

Applications note

WebSIDD: server for predicting stress-induced duplex destabilized (SIDD) sites in superhelical DNA

Chengpeng Bi 1 Craig J. Benham 1*

1 UC Davis Genome Center, University of California, One Shields Avenue, Davis CA 95616

* To whom correspondence should be addressed. E-mail: cjbenham{at}ucdavis.edu.


  Abstract

Summary: WebSIDD is a web-based service designed to predict locations and extents of stress-induced duplex destabilization (SIDD) that occur in a double-stranded DNA molecule of specified base sequence, on which a specified level of superhelical stress is imposed. The algorithm calculates the approximate equilibrium statistical mechanical distribution of a population of identical molecules among its accessible states. The user inputs the DNA sequence, and the program outputs the calculated transition probability and destabilization energy of each base pair in the sequence. As options, the user can specify the temperature and the level of superhelicity. The values of all structural and energy parameters used in the calculation have been experimentally measured. WebSIDD should prove useful for finding SIDD-susceptible sites in genomic sequences, and correlating their occurrence with locations involved in regulatory and pathological processes. This strategy already has illuminated the roles of SIDD in diverse biological regulatory processes, including transcriptional initiation and termination, and the eukaryotic nuclear scaffold attachments that partition chromosomes into domains.

Availability: http://orange.genomecenter.ucdavis.edu/benham/sidd/index.html.


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