N-Gram characterization of genomic islands in bacterial genomes.

ABSTRACT: The paper presents a novel, n-gram-based method for analysis of bacterial genome segments known as genomic islands (GIs). Identification of GIs in bacterial genomes is an important task since many of them represent inserts that may contribute to bacterial evolution and pathogenesis. In order to characterize and distinguish GIs from rest of the genome, binary classification of islands based on n-gram frequency distribution have been performed. It consists of testing the agreement of islands n-gram frequency distributions with the complete genome and backbone sequence. In addition, a statistic based on the maximal order Markov model is used to identify significantly overrepresented and underrepresented n-grams in islands. The results may be used as a basis for Zipf-like analysis suggesting t

SUBMITTER: Pavlovic-Lazetic GM 

PROVIDER: S-EPMC7185697 | biostudies-literature | 2009 Mar

REPOSITORIES: biostudies-literature