Application of sliding-window discretization and minimization of stochastic complexity for the analysis of fAFLP genotyping fingerprint patterns of Vibrionaceae.
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.
Dawyndt
Peter
P
Laboratorium voor Microbiologie, Universiteit Gent, B-9000 Gent, Belgium.
Thompson
Fabiano L
FL
Laboratorium voor Microbiologie, Universiteit Gent, B-9000 Gent, Belgium.
Austin
Brian
B
School of Life Sciences, Heriot-Watt University, Edinburgh EH14 4AS, UK.
Swings
Jean
J
Laboratorium voor Microbiologie, Universiteit Gent, B-9000 Gent, Belgium.
Koski
Timo
T
Department of Mathematics, University of Linköping, S-58183 Linköping, Sweden.
Gyllenberg
Mats
M
Department of Mathematics, University of Turku, FIN-20014 Turku, Finland.
D000465:Algorithms; D015373:Bacterial Typing Techniques; D016172:DNA Fingerprinting / Q000379:methods*; D005838:Genotype; D012150:Polymorphism, Restriction Fragment Length; D012984:Software; D013269:Stochastic Processes; D014737:Vibrionaceae / Q000145:classification* / Q000235:genetics