Title

Shewregdb: Database and visualization environment for experimental and predicted regulatory information in Shewanella oneidensis mr-1

Authors

Mustafa H. Syed^1*, Tatiana V. Karpinets^1,2, Michael R. Leuze¹, Guruprasad H. Kora^1,2, Margaret R. Romine³, Edward C. Uberbacher¹

Affiliation

¹Oak Ridge National Laboratory, Oak Ridge, Tennessee, 37831, U.S.A; ²University of Tennessee, Knoxville, Tennessee, 37996, U.S.A; ³Pacific Northwest National Laboratory, Richland, Washington, 99352, U.S.A

Email

syedmh@ornl.gov

Article Type

Database

Date

Received May 27, 2009; Revised July 20, 2009; Accepted September 11, 2009; Published October 15, 2009

Abstract

Shewanella oneidensis MR-1 is an important model organism for environmental research as it has an exceptional metabolic and respiratory versatility regulated by a complex regulatory network. We have developed a database to collect experimental and computational data relating to regulation of gene and protein expression, and, a visualization environment that enables integration of these data types. The regulatory information in the database includes predictions of DNA regulator binding sites, sigma factor binding sites, transcription units, operons, promoters, and RNA regulators including non-coding RNAs, riboswitches, and different types of terminators.

Keywords

Citation

Syed et al., Bioinformation 4(4): 169-172 (2009)

Edited by

P. Kangueane

ISSN

0973-2063

Publisher

Biomedical Informatics

License

This is an Open Access article which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. This is distributed under the terms of the Creative Commons Attribution License.