Skip Navigation


Bioinformatics Advance Access originally published online on September 5, 2007
Bioinformatics 2007 23(20):2760-2767; doi:10.1093/bioinformatics/btm446
This Article
Right arrow Full Text Freely available
Right arrow FREE Full Text (Print PDF) Freely available
Right arrow Supplementary data
Right arrowOA All Versions of this Article:
23/20/2760    most recent
btm446v2
btm446v1
Right arrow Comments: Submit a response
Right arrow Alert me when this article is cited
Right arrow Alert me when Comments are posted
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in ISI Web of Science
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrow Search for citing articles in:
ISI Web of Science (11)
Google Scholar
Right arrow Articles by Cai, Y.
Right arrow Articles by Peccoud, J.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Cai, Y.
Right arrow Articles by Peccoud, J.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

© 2007 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.

A syntactic model to design and verify synthetic genetic constructs derived from standard biological parts

Yizhi Cai 1, Brian Hartnett 1, Claes Gustafsson 2 and Jean Peccoud 1,*

1Virginia Bioinformatics Institute, Virginia Polytechnic Institute and State University, Washington Street, MC 0477, Blacksburg VA 24061, USA and 2DNA2.0 Inc. 1430 O’Brien Drive Suite E, Menlo Park CA 94025, USA

*To whom correspondence should be addressed.


  Abstract

Motivation: The sequence of artificial genetic constructs is composed of multiple functional fragments, or genetic parts, involved in different molecular steps of gene expression mechanisms. Biologists have deciphered structural rules that the design of genetic constructs needs to follow in order to ensure a successful completion of the gene expression process, but these rules have not been formalized, making it challenging for non-specialists to benefit from the recent progress in gene synthesis.

Results: We show that context-free grammars (CFG) can formalize these design principles. This approach provides a path to organizing libraries of genetic parts according to their biological functions, which correspond to the syntactic categories of the CFG. It also provides a framework for the systematic design of new genetic constructs consistent with the design principles expressed in the CFG. Using parsing algorithms, this syntactic model enables the verification of existing constructs. We illustrate these possibilities by describing a CFG that generates the most common architectures of genetic constructs in Escherichia coli.

Availability: A web site allows readers to experiment with the algorithms presented in this article: www.genocad.org

Contact: peccoud{at}vt.edu

Supplementary information: Sequences and models are available at Bioinformatics online.

Associate Editor: John Quackenbush

Received on July 3, 2007; revised on August 20, 2007; accepted on August 21, 2007

Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?


This article has been cited by other articles:


Home page
 J R Soc InterfaceHome page
M. Pedersen and A. Phillips
Towards programming languages for genetic engineering of living cells
J R Soc Interface, August 6, 2009; 6(Suppl_4): S437 - S450.
[Abstract] [Full Text] [PDF]

Home page
 J R Soc InterfaceHome page
Y. Matsuoka, S. Ghosh, and H. Kitano
Consistent design schematics for biological systems: standardization of representation in biological engineering
J R Soc Interface, August 6, 2009; 6(Suppl_4): S393 - S404.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
M. J. Czar, Y. Cai, and J. Peccoud
Writing DNA with GenoCADTM
Nucleic Acids Res., July 1, 2009; 37(suppl_2): W40 - W47.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
M.A. Marchisio and J. Stelling
Computational design of synthetic gene circuits with composable parts
Bioinformatics, September 1, 2008; 24(17): 1903 - 1910.
[Abstract] [Full Text] [PDF]


Disclaimer: Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.