Virginia Tech
    • Log in
    View Item 
    •   VTechWorks Home
    • Fralin Life Sciences Institute
    • Scholarly Works, Fralin Life Sciences Institute
    • View Item
    •   VTechWorks Home
    • Fralin Life Sciences Institute
    • Scholarly Works, Fralin Life Sciences Institute
    • View Item
    JavaScript is disabled for your browser. Some features of this site may not work without it.

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

    Thumbnail
    View/Open
    2007_Bioinformatics_Cai_grammar.zip (131.0Kb)
    Downloads: 63
    Parts list in fasta format (31.18Kb)
    Downloads: 127
    Date
    2007
    Author
    Cai, Y.
    Hartnett, B.
    Gustafsson, C.
    Peccoud, Jean
    Metadata
    Show full item record
    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
    URI
    http://hdl.handle.net/10919/18672
    Collections
    • Scholarly Works, Fralin Life Sciences Institute [542]

    If you believe that any material in VTechWorks should be removed, please see our policy and procedure for Requesting that Material be Amended or Removed. All takedown requests will be promptly acknowledged and investigated.

    Virginia Tech | University Libraries | Contact Us
     

     

    VTechWorks

    AboutPoliciesHelp

    Browse

    All of VTechWorksCommunities & CollectionsBy Issue DateAuthorsTitlesSubjectsThis CollectionBy Issue DateAuthorsTitlesSubjects

    My Account

    Log inRegister

    Statistics

    View Usage Statistics

    If you believe that any material in VTechWorks should be removed, please see our policy and procedure for Requesting that Material be Amended or Removed. All takedown requests will be promptly acknowledged and investigated.

    Virginia Tech | University Libraries | Contact Us