Modeling structure-function relationships in synthetic DNA sequences using attribute grammars.

Recognizing that certain biological functions can be associated with specific DNA sequences has led various fields of biology to adopt the notion of the genetic part. This concept provides a finer level of granularity than the traditional notion of the gene. However, a method of formally relating ho...

Descripción completa

Guardado en:

Detalles Bibliográficos
Autores principales:	Yizhi Cai, Matthew W Lux, Laura Adam, Jean Peccoud
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2009
Materias:	Biology (General) QH301-705.5
Acceso en línea:	https://doaj.org/article/52714c0810d7425f8b7ab7effc2b89a6
Etiquetas:	Agregar Etiqueta Sin Etiquetas, Sea el primero en etiquetar este registro!

id	oai:doaj.org-article:52714c0810d7425f8b7ab7effc2b89a6
record_format	dspace
spelling	oai:doaj.org-article:52714c0810d7425f8b7ab7effc2b89a62021-11-25T05:42:07ZModeling structure-function relationships in synthetic DNA sequences using attribute grammars.1553-734X1553-735810.1371/journal.pcbi.1000529https://doaj.org/article/52714c0810d7425f8b7ab7effc2b89a62009-10-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/19816554/?tool=EBIhttps://doaj.org/toc/1553-734Xhttps://doaj.org/toc/1553-7358Recognizing that certain biological functions can be associated with specific DNA sequences has led various fields of biology to adopt the notion of the genetic part. This concept provides a finer level of granularity than the traditional notion of the gene. However, a method of formally relating how a set of parts relates to a function has not yet emerged. Synthetic biology both demands such a formalism and provides an ideal setting for testing hypotheses about relationships between DNA sequences and phenotypes beyond the gene-centric methods used in genetics. Attribute grammars are used in computer science to translate the text of a program source code into the computational operations it represents. By associating attributes with parts, modifying the value of these attributes using rules that describe the structure of DNA sequences, and using a multi-pass compilation process, it is possible to translate DNA sequences into molecular interaction network models. These capabilities are illustrated by simple example grammars expressing how gene expression rates are dependent upon single or multiple parts. The translation process is validated by systematically generating, translating, and simulating the phenotype of all the sequences in the design space generated by a small library of genetic parts. Attribute grammars represent a flexible framework connecting parts with models of biological function. They will be instrumental for building mathematical models of libraries of genetic constructs synthesized to characterize the function of genetic parts. This formalism is also expected to provide a solid foundation for the development of computer assisted design applications for synthetic biology.Yizhi CaiMatthew W LuxLaura AdamJean PeccoudPublic Library of Science (PLoS)articleBiology (General)QH301-705.5ENPLoS Computational Biology, Vol 5, Iss 10, p e1000529 (2009)
institution	DOAJ
collection	DOAJ
language	EN
topic	Biology (General) QH301-705.5
spellingShingle	Biology (General) QH301-705.5 Yizhi Cai Matthew W Lux Laura Adam Jean Peccoud Modeling structure-function relationships in synthetic DNA sequences using attribute grammars.
description	Recognizing that certain biological functions can be associated with specific DNA sequences has led various fields of biology to adopt the notion of the genetic part. This concept provides a finer level of granularity than the traditional notion of the gene. However, a method of formally relating how a set of parts relates to a function has not yet emerged. Synthetic biology both demands such a formalism and provides an ideal setting for testing hypotheses about relationships between DNA sequences and phenotypes beyond the gene-centric methods used in genetics. Attribute grammars are used in computer science to translate the text of a program source code into the computational operations it represents. By associating attributes with parts, modifying the value of these attributes using rules that describe the structure of DNA sequences, and using a multi-pass compilation process, it is possible to translate DNA sequences into molecular interaction network models. These capabilities are illustrated by simple example grammars expressing how gene expression rates are dependent upon single or multiple parts. The translation process is validated by systematically generating, translating, and simulating the phenotype of all the sequences in the design space generated by a small library of genetic parts. Attribute grammars represent a flexible framework connecting parts with models of biological function. They will be instrumental for building mathematical models of libraries of genetic constructs synthesized to characterize the function of genetic parts. This formalism is also expected to provide a solid foundation for the development of computer assisted design applications for synthetic biology.
format	article
author	Yizhi Cai Matthew W Lux Laura Adam Jean Peccoud
author_facet	Yizhi Cai Matthew W Lux Laura Adam Jean Peccoud
author_sort	Yizhi Cai
title	Modeling structure-function relationships in synthetic DNA sequences using attribute grammars.
title_short	Modeling structure-function relationships in synthetic DNA sequences using attribute grammars.
title_full	Modeling structure-function relationships in synthetic DNA sequences using attribute grammars.
title_fullStr	Modeling structure-function relationships in synthetic DNA sequences using attribute grammars.
title_full_unstemmed	Modeling structure-function relationships in synthetic DNA sequences using attribute grammars.
title_sort	modeling structure-function relationships in synthetic dna sequences using attribute grammars.
publisher	Public Library of Science (PLoS)
publishDate	2009
url	https://doaj.org/article/52714c0810d7425f8b7ab7effc2b89a6
work_keys_str_mv	AT yizhicai modelingstructurefunctionrelationshipsinsyntheticdnasequencesusingattributegrammars AT matthewwlux modelingstructurefunctionrelationshipsinsyntheticdnasequencesusingattributegrammars AT lauraadam modelingstructurefunctionrelationshipsinsyntheticdnasequencesusingattributegrammars AT jeanpeccoud modelingstructurefunctionrelationshipsinsyntheticdnasequencesusingattributegrammars
_version_	1718414517037170688

Modeling structure-function relationships in synthetic DNA sequences using attribute grammars.

Ejemplares similares