TY - JOUR T1 - Modeling Structure-Function Relationships in Synthetic DNA Sequences using Attribute Grammars A1 - Cai, Yizhi A1 - Lux, Matthew W. A1 - Adam, Laura A1 - Peccoud, Jean Y1 - 2009/10/09 N2 - Author Summary Deciphering the genetic code has been one of the major milestones in our understanding of how genetic information is stored in DNA sequences. However, only part of the genetic information is captured by the simple rules describing the correspondence between gene and proteins. The molecular mechanisms of gene expression are now understood well enough to recognize that DNA sequences are rich in functional blocks that do not code for proteins. It has proved difficult to express the function of these genetic parts in a computer readable format that could be used to predict the emerging behavior of DNA sequences combining multiple interacting parts. We are showing that methods used by computer scientists to develop programming languages can be applied to DNA sequences. They provide a framework to: 1) express the biological functions of genetic parts, 2) how these functions depend on the context in which the parts are placed, and 3) translate DNA sequences composed of multiple parts into a model predicting how the DNA sequence will behave in vivo. Our approach provides a formal representation of how the biological function of genetic parts can be used to assist in the engineering of synthetic DNA sequences by automatically generating models of the design for analysis. JF - PLOS Computational Biology JA - PLOS Computational Biology VL - 5 IS - 10 UR - https://doi.org/10.1371/journal.pcbi.1000529 SP - e1000529 EP - PB - Public Library of Science M3 - doi:10.1371/journal.pcbi.1000529 ER -