Beyond similarity assessment: Selecting the optimal model for sequence alignment via the Factorized Asymptotic Bayesian algorithm

Taikai Takeda, Michiaki Hamada

    Research output: Contribution to journalArticle


    Motivation Pair Hidden Markov Models (PHMMs) are probabilistic models used for pairwise sequence alignment, a quintessential problem in bioinformatics. PHMMs include three types of hidden states: match, insertion and deletion. Most previous studies have used one or two hidden states for each PHMM state type. However, few studies have examined the number of states suitable for representing sequence data or improving alignment accuracy. Results We developed a novel method to select superior models (including the number of hidden states) for PHMM. Our method selects models with the highest posterior probability using Factorized Information Criterion, which is widely utilized in model selection for probabilistic models with hidden variables. Our simulations indicated that this method has excellent model selection capabilities with slightly improved alignment accuracy. We applied our method to DNA datasets from 5 and 28 species, ultimately selecting more complex models than those used in previous studies. Availability and implementation The software is available at Contact Supplementary informationSupplementary dataare available at Bioinformatics online.

    Original languageEnglish
    Pages (from-to)576-584
    Number of pages9
    Issue number4
    Publication statusPublished - 2018 Feb 15


    ASJC Scopus subject areas

    • Statistics and Probability
    • Biochemistry
    • Molecular Biology
    • Computer Science Applications
    • Computational Theory and Mathematics
    • Computational Mathematics

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