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SIDDBase


NAR Molecular Biology Database Collection entry number 866
Wang H., Kaloper M. and Benham C.J.
UC Davis Genome Center, University of California at Davis, One Shields Avenue, Davis, CA 95616

Database Description

SIDDBASE (http://www.genomecenter.ucdavis.edu/benham/siddbase) is a database of stress induced DNA destabilization (SIDD) properties of various complete microbial genomes. SIDD sites are locations in genomic DNA which are predicted to become susceptible to duplex strand separation under supehelical stress. This is a potentially important DNA structural property, which is known to be involved in several regulatory mechanisms. Specific SIDD sites play important roles in transcriptional regulation, replication, chromosomal matrix attachment and other biological processes. This structural approach is an alternative to the usual DNA lexical content analysis. It is also fundamentally different from DNA thermal stability which only considers local thermodynamic stability or A+T content. The SIDDBASE database currently contains SIDD profiles of 138 prokaryotic and archaeal genomes. It can be queried by the genome, and then either by chromosomal location or gene name.

Recent Developments

We plan to expand the database to include more microbial genomes as their analyses are completed. We also intend to include eukaryotic genomes.

Acknowledgements

This work was supported by the National Science Foundation (DBI-0416764) and the NIH (RO1-GM68903).


Go to the abstract in the NAR 2006 Database Issue.
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