title: SGDB: a database of synthetic genes re-designed for optimizing protein over-expression.
abstract: 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.
authors.affiliation: Department of Biological Sciences, University of Maryland at Baltimore County, 1000 Hilltop Circle, Baltimore, MD 21229, USA.
authors.forename: Gang
authors.initials: G
authors.lastname: Wu
authors.forename: Yuanpu
authors.initials: Y
authors.lastname: Zheng
authors.forename: Imran
authors.initials: I
authors.lastname: Qureshi
authors.forename: Htar Thant
authors.initials: HT
authors.lastname: Zin
authors.forename: Tyler
authors.initials: T
authors.lastname: Beck
authors.forename: Blazej
authors.initials: B
authors.lastname: Bulka
authors.forename: Stephen J
authors.initials: SJ
authors.lastname: Freeland
mesh_terms: D030561:Databases, Nucleic Acid; D005813:Genes, Synthetic; D020407:Internet; D014176:Protein Biosynthesis; D014584:User-Computer Interface