Computational grammars for interrogation of genomes

Jaron Schaeffer*, Afra Held, Guy Tsafnat

*Corresponding author for this work

Research output: Chapter in Book/Report/Conference proceedingChapterpeer-review

3 Citations (Scopus)


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.

Original languageEnglish
Title of host publicationInfectious Disease Informatics
EditorsVitali Sintchenko
Place of PublicationNew York
PublisherSpringer, Springer Nature
Number of pages16
ISBN (Electronic)9781441913272
ISBN (Print)9781441913265
Publication statusPublished - 2010
Externally publishedYes


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