Antibiotic resistance genes are embedded in mobile genetic elements (MGEs) that spread genes between organisms, even of different species. MGEs are large structures that consist of genes, and protein interaction sites. Although a considerable number of microbial DNA sequences have been published, searching for multi-resistant MGEs remains largely a manual task. This usually involves BLAST searches and a combination of keyword-based searches through sequence annotations and the literature. Using computational grammars, we can automate the recognition of arbitrarily complex sequence structures. In this chapter, we describe computational grammars, showing how they can be used to automate MGE annotation, and give examples of the annotation enabled by such grammars.
|Title of host publication||Infectious Disease Informatics|
|Place of Publication||New York|
|Publisher||Springer, Springer Nature|
|Number of pages||16|
|Publication status||Published - 2010|