Please use this identifier to cite or link to this item: http://hdl.handle.net/1893/7362
Appears in Collections:Aquaculture Journal Articles
Peer Review Status: Refereed
Title: Application of sliding-window discretization and minimization of stochastic complexity for the analysis of fAFLP genotyping fingerprint patterns of Vibrionaceae
Authors: Dawyndt, Peter
Thompson, Fabiano L
Austin, Brian
Swings, Jean
Koski, Timo
Gyllenberg, Mats
Contact Email: brian.austin@stir.ac.uk
Keywords: fAFLP
Fluorescent amplified fragment length polymorphism HMO
Hypothetical median organism SC
Stochastic complexity
Issue Date: Jan-2005
Publisher: Society for General Microbiology
Citation: Dawyndt P, Thompson FL, Austin B, Swings J, Koski T & Gyllenberg M (2005) Application of sliding-window discretization and minimization of stochastic complexity for the analysis of fAFLP genotyping fingerprint patterns of Vibrionaceae, International Journal of Systematic and Evolutionary Microbiology, 55 (1), pp. 57-66.
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.
Type: Journal Article
URI: http://hdl.handle.net/1893/7362
DOI Link: http://dx.doi.org/10.1099/ijs.0.63136-0
Rights: The publisher does not allow this work to be made publicly available in this Repository. Please use the Request a Copy feature at the foot of the Repository record to request a copy directly from the author. You can only request a copy if you wish to use this work for your own research or private study.
Affiliation: Ghent University
Aquaculture
Ghent University
Linkoping University
University of Turku

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