SGDB: a database of synthetic genes re-designed for optimizing protein over-expression
| dc.contributor.author | Wu, Gang | |
| dc.contributor.author | Zheng, Yuanpu | |
| dc.contributor.author | Qureshi, Imran | |
| dc.contributor.author | Zin, Htar Thant | |
| dc.contributor.author | Beck, Tyler | |
| dc.contributor.author | Bulka, Blazej | |
| dc.contributor.author | Freeland, Stephen J. | |
| dc.date.accessioned | 2023-07-18T19:24:15Z | |
| dc.date.available | 2023-07-18T19:24:15Z | |
| dc.date.issued | 2006-11-07 | |
| dc.description.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. | en_US |
| dc.description.sponsorship | This project is supported by NSF award 0317349 (to S.J.F.) from DBI (Biological Databases and Informatics) Program. The authors thank Dr Alex Bateman, Dr Philip Farabaugh, Dr Janice Zengel, and two anonymous reviewers for insights and comments that have improved this database and manuscript. Funding to pay the Open Access publication charges for this article was provided by US National Science Foundation. | en_US |
| dc.description.uri | https://academic.oup.com/nar/article/35/suppl_1/D76/1088335 | en_US |
| dc.format.extent | 4 pages | en_US |
| dc.genre | journal articles | en_US |
| dc.identifier | doi:10.13016/m2k7ba-5bcq | |
| dc.identifier.citation | Gang Wu and others, SGDB: a database of synthetic genes re-designed for optimizing protein over-expression, Nucleic Acids Research, Volume 35, Issue suppl_1, 1 January 2007, Pages D76–D79, https://doi.org/10.1093/nar/gkl648 | en_US |
| dc.identifier.uri | https://doi.org/10.1093/nar/gkl648 | |
| dc.identifier.uri | http://hdl.handle.net/11603/28739 | |
| dc.language.iso | en_US | en_US |
| dc.publisher | Oxford University Press | en_US |
| dc.relation.isAvailableAt | The University of Maryland, Baltimore County (UMBC) | |
| dc.relation.ispartof | UMBC Biological Sciences Department Collection | |
| dc.relation.ispartof | UMBC Faculty Collection | |
| dc.relation.ispartof | UMBC Student Collection | |
| dc.relation.ispartof | UMBC Computer Science and Electrical Engineering Department | |
| dc.relation.ispartof | UMBC Individualized Study Program (INDS) | |
| dc.rights | This item is likely protected under Title 17 of the U.S. Copyright Law. Unless on a Creative Commons license, for uses protected by Copyright Law, contact the copyright holder or the author. | en_US |
| dc.rights | Attribution-NonCommercial 2.0 UK: England & Wales (CC BY-NC 2.0 UK) | * |
| dc.rights.uri | https://creativecommons.org/licenses/by-nc/2.0/uk/ | * |
| dc.title | SGDB: a database of synthetic genes re-designed for optimizing protein over-expression | en_US |
| dc.type | Text | en_US |
| dcterms.creator | https://orcid.org/0000-0002-1678-5864 | en_US |
| dcterms.creator | https://orcid.org/0000-0002-7373-0640 | en_US |