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Nucleic Acids Research Advance Access first published online on October 24, 2006
This version published online on November 7, 2006
Nucleic Acids Research, doi:10.1093/nar/gkl648
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© 2006 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Database Issue

SGDB: a database of synthetic genes re-designed for optimizing protein over-expression

Gang Wu, Yuanpu Zheng, Imran Qureshi, Htar Thant Zin, Tyler Beck, Blazej Bulka1 and Stephen J. Freeland*

Department of Biological Sciences, University of Maryland at Baltimore County 1000 Hilltop Circle, Baltimore, MD 21229, USA 1 Department of Computer Sciences, University of Maryland at Baltimore County 1000 Hilltop Circle, Baltimore, MD 21229, USA

*To whom correspondence should be addressed. Tel: +1 410 455 2231; Fax: +1 410 455 3875; Email: freeland{at}umbc.edu

Received June 22, 2006. Revised June 22, 2006. Accepted August 23, 2006.

Here we present the Synthetic Gene Database (SGDB): a relational database that houses sequences and associated experimental information on synthetic (artificially engineered) genes from all peer-reviewed studies published to date. At present, the database comprises information from more than 200 published experiments. This resource not only provides reference material to guide experimentalists in designing new genes that improve protein expression, but also offers a dataset for analysis by bioinformaticians who seek to test ideas regarding the underlying factors that influence gene expression. The SGDB was built under MySQL database management system. We also offer an XML schema for standardized data description of synthetic genes. Users can access the database at http://www.evolvingcode.net/codon/sgdb/index.php, or batch downloads all information through XML files. Moreover, users may visually compare the coding sequences of a synthetic gene and its natural counterpart with an integrated web tool at http://www.evolvingcode.net/codon/sgdb/aligner.php, and discuss questions, findings and related information on an associated e-forum at http://www.evolvingcode.net/forum/viewforum.php?f=27.


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