Application of sliding window discretization and minimization of stochastic complexity for the analysis of FAFLP genotyping fingerprint patterns of vibrionaceae

Peter Dawyndt, Fabiano L. Thompson, Brian Austin, Jean Swings, Timo Koski, Mats Gyllenberg

    Research output: Contribution to journalArticle

    Abstract

    Minimization of stochastic complexity (SC) was used as a method for classification of genotypic fingerprints. The method was applied to fluorescent amplified fragment length polymorphism (fAFLP) fingerprint patterns of 507 Vibrionaceae representatives. As the current BinClass implementation of the optimization algorithm for classification only works on binary vectors, the original fingerprints were discretized in a preliminary step using the sliding-window band-matching method, in order to maximally preserve the information content of the original band patterns. The novel classification generated using the BinClass software package was subjected to an in-depth comparison with a hierarchical classification of the same dataset, in order to acknowledge the applicability of the new classification method as a more objective algorithm for the classification of genotyping fingerprint patterns. Recent DNA-DNA hybridization and 16S rRNA gene sequence experiments proved that the classification based on SC-minimization forms separate clusters that contain the fAFLP patterns for all representatives of the species Enterovibrio norvegicus, Vibrio fortis, Vibrio diazotrophicus or Vibrio campbellii, while previous hierarchical cluster analysis had suggested more heterogeneity within the fAFLP patterns by splitting the representatives of the above-mentioned species into multiple distant clusters. As a result, the new classification methodology has highlighted some previously unseen relationships within the biodiversity of the family Vibrionaceae. © 2005 IUMS.

    Original languageEnglish
    Pages (from-to)57-66
    Number of pages10
    JournalInternational Journal of Systematic and Evolutionary Microbiology
    Volume55
    Issue number1
    DOIs
    Publication statusPublished - Jan 2005

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    Vibrionaceae
    Dermatoglyphics
    Systems Analysis
    Vibrio
    Biodiversity
    DNA
    rRNA Genes
    Cluster Analysis
    Software

    Cite this

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    title = "Application of sliding window discretization and minimization of stochastic complexity for the analysis of FAFLP genotyping fingerprint patterns of vibrionaceae",
    abstract = "Minimization of stochastic complexity (SC) was used as a method for classification of genotypic fingerprints. The method was applied to fluorescent amplified fragment length polymorphism (fAFLP) fingerprint patterns of 507 Vibrionaceae representatives. As the current BinClass implementation of the optimization algorithm for classification only works on binary vectors, the original fingerprints were discretized in a preliminary step using the sliding-window band-matching method, in order to maximally preserve the information content of the original band patterns. The novel classification generated using the BinClass software package was subjected to an in-depth comparison with a hierarchical classification of the same dataset, in order to acknowledge the applicability of the new classification method as a more objective algorithm for the classification of genotyping fingerprint patterns. Recent DNA-DNA hybridization and 16S rRNA gene sequence experiments proved that the classification based on SC-minimization forms separate clusters that contain the fAFLP patterns for all representatives of the species Enterovibrio norvegicus, Vibrio fortis, Vibrio diazotrophicus or Vibrio campbellii, while previous hierarchical cluster analysis had suggested more heterogeneity within the fAFLP patterns by splitting the representatives of the above-mentioned species into multiple distant clusters. As a result, the new classification methodology has highlighted some previously unseen relationships within the biodiversity of the family Vibrionaceae. {\circledC} 2005 IUMS.",
    author = "Peter Dawyndt and Thompson, {Fabiano L.} and Brian Austin and Jean Swings and Timo Koski and Mats Gyllenberg",
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    Application of sliding window discretization and minimization of stochastic complexity for the analysis of FAFLP genotyping fingerprint patterns of vibrionaceae. / Dawyndt, Peter; Thompson, Fabiano L.; Austin, Brian; Swings, Jean; Koski, Timo; Gyllenberg, Mats.

    In: International Journal of Systematic and Evolutionary Microbiology, Vol. 55, No. 1, 01.2005, p. 57-66.

    Research output: Contribution to journalArticle

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