Clustering DNA sequences using the out-of-place measure with reduced n-grams

Hsin-Hsiung Huang, Chenglong Yu

    Research output: Contribution to journalArticlepeer-review

    11 Citations (Scopus)


    The alignment-free n-gram based method with the out-of-place measures as the distance has been successfully applied to automatic text or natural languages categorization in real time. However, it is not clear about its performance and the selection of n for comparing genome sequences. Here we propose a symmetric version of the out-of-place measure and a new approach for finding the optimal range of n to construct a phylogenetic tree with the symmetric out-of-place measures. Our method is then applied to real genome sequence datasets. The resulting phylogenetic trees are matching with the standard biological classification. It shows that our proposed method is a very powerful tool for phylogenetic analysis in terms of both classification accuracy and computation efficiency.

    Original languageEnglish
    Pages (from-to)61-72
    Number of pages12
    JournalJournal of Theoretical Biology
    Publication statusPublished - 7 Oct 2016


    • Alignment-free method
    • Out-of-place measure
    • Phylogenetic analysis
    • Reduced n-gram


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