Context-driven discovery of gene cassettes in mobile integrons using a computational grammar.

ABSTRACT:

Background

Gene discovery algorithms typically examine sequence data for low level patterns. A novel method to computationally discover higher order DNA structures is presented, using a context sensitive grammar. The algorithm was applied to the discovery of gene cassettes associated with integrons. The discovery and annotation of antibiotic resistance genes in such cassettes is essential for effective monitoring of antibiotic resistance patterns and formulation of public health antibiotic prescription policies.

Results

We discovered two new putative gene cassettes using the method, from 276 integron features and 978 GenBank sequences. The system achieved kappa = 0.972 annotation agreement with an expert gold standard of 300 sequences. In rediscovery experiments, we deleted

SUBMITTER: Tsafnat G 

PROVIDER: S-EPMC3087341 | biostudies-literature | 2009 Sep

REPOSITORIES: biostudies-literature