Effective text compression with simultaneous digram and trigram encoding
Journal of Information Science
A Dictionary for Minimum Redundancy Encoding
Journal of the ACM (JACM)
Spss Programming And Data Management: A Guide for Spss And Sas Users
Spss Programming And Data Management: A Guide for Spss And Sas Users
Comparative n-gram analysis of whole-genome protein sequences
HLT '02 Proceedings of the second international conference on Human Language Technology Research
Introduction to Information Retrieval
Introduction to Information Retrieval
Could n-gram analysis contribute to genomic island determination?
Journal of Biomedical Informatics
Managing misspelled queries in IR applications
Information Processing and Management: an International Journal
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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 that some of the n-grams are overrepresented in a subset of islands and underrepresented in the backbone, or vice versa, thus complementing the binary classification. The method is applied to strain-specific regions in the Escherichia coli O157:H7 EDL933 genome (O-islands), resulting in two groups of O-islands with different n-gram characteristics. It refines a characterization based on other compositional features such as G+C content and codon usage, and may help in identification of GIs, and also in research and development of adequate drugs targeting virulence genes in them.