Skip Navigation


Bioinformatics Advance Access originally published online on May 6, 2004
This Article
Right arrow FREE Full Text (Print PDF) Freely available
Right arrow FREE Full Text (Screen PDF)
Right arrow All Versions of this Article:
20/9/1477    most recent
bth304v1
Right arrow Comments: Submit a response
Right arrow Alert me when this article is cited
Right arrow Alert me when Comments are posted
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in ISI Web of Science
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrow Search for citing articles in:
ISI Web of Science (26)
Right arrowRequest Permissions
Google Scholar
Right arrow Articles by Bi, C.
Right arrow Articles by Benham, C. J.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Bi, C.
Right arrow Articles by Benham, C. J.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

Bioinformatics 20(9) © Oxford University Press 2004; all rights reserved.

Applications Note

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

Chengpeng Bi {dagger} and Craig J. Benham *

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

Received on May 8, 2003; revised on June 11, 2003; accepted on July 29, 2003
Advance Access Publication May 6, 2004

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

Contact: cjbenham{at}ucdavis.edu

* To whom correspondence should be addressed.

{dagger} Present address: Laboratory of Human Molecular Genetics, Children's Mercy Hospital and Clinics, Kansas City, MO 64108, USA.


Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?


This article has been cited by other articles:


Home page
 J. Bacteriol.Home page
A. Zomer, M. Fernandez, B. Kearney, G. F. Fitzgerald, M. Ventura, and D. van Sinderen
An Interactive Regulatory Network Controls Stress Response in Bifidobacterium breve UCC2003
J. Bacteriol., November 15, 2009; 191(22): 7039 - 7049.
[Abstract] [Full Text] [PDF]

Home page
 MicrobiologyHome page
F. P. Douillard, K. A. Ryan, J. Hinds, and P. W. O'Toole
Effect of FliK mutation on the transcriptional activity of the {sigma}54 sigma factor RpoN in Helicobacter pylori
Microbiology, June 1, 2009; 155(6): 1901 - 1911.
[Abstract] [Full Text] [PDF]

Home page
 Proc. Natl. Acad. Sci. USAHome page
L. R. Benjamin, H.-J. Chung, S. Sanford, F. Kouzine, J. Liu, and D. Levens
Hierarchical mechanisms build the DNA-binding specificity of FUSE binding protein
PNAS, November 25, 2008; 105(47): 18296 - 18301.
[Abstract] [Full Text] [PDF]

Home page
 Mol. Cell. Biol.Home page
G. Liu, J. J. Bissler, R. R. Sinden, and M. Leffak
Unstable Spinocerebellar Ataxia Type 10 (ATTCT){middle dot}(AGAAT) Repeats Are Associated with Aberrant Replication at the ATX10 Locus and Replication Origin-Dependent Expansion at an Ectopic Site in Human Cells
Mol. Cell. Biol., November 15, 2007; 27(22): 7828 - 7838.
[Abstract] [Full Text] [PDF]

Home page
 J. Bacteriol.Home page
R. Gonzalez-Soltero, E. Botello, and A. Jimenez-Sanchez
Initiation of Heat-Induced Replication Requires DnaA and the L-13-mer of oriC
J. Bacteriol., December 1, 2006; 188(23): 8294 - 8298.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
H. Wang, M. Kaloper, and C. J. Benham
SIDDBASE: a database containing the stress-induced DNA duplex destabilization (SIDD) profiles of complete microbial genomes
Nucleic Acids Res., January 1, 2006; 34(suppl_1): D373 - D378.
[Abstract] [Full Text] [PDF]

Home page
 J. Med. Genet.Home page
R Visser, O Shimokawa, N Harada, N Niikawa, and N Matsumoto
Non-hotspot-related breakpoints of common deletions in Sotos syndrome are located within destabilised DNA regions
J. Med. Genet., November 1, 2005; 42(11): e66 - e66.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
E. Tostesen, G. I. Jerstad, and E. Hovig
Stitchprofiles.uio.no: analysis of partly melted DNA conformations using stitch profiles
Nucleic Acids Res., July 1, 2005; 33(suppl_2): W573 - W576.
[Abstract] [Full Text] [PDF]


Disclaimer: Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.