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Soft topographic map for clustering and classification of bacteria

By Massimo La Rosa, Giuseppe Di Fatta, Salvatore Gaglio, Giovanni M Giammanco, Riccardo Rizzo and Alfonso M. Urso

Abstract

In this work a new method for clustering and building a\ud topographic representation of a bacteria taxonomy is presented. The method is based on the analysis of stable parts of the genome, the so-called “housekeeping genes”. The proposed method generates topographic maps of the bacteria taxonomy, where relations among different\ud type strains can be visually inspected and verified. Two well known DNA alignement algorithms are applied to the genomic sequences. Topographic maps are optimized to represent the similarity among the sequences according to their evolutionary distances. The experimental analysis is carried out on 147 type strains of the Gammaprotebacteria\ud class by means of the 16S rRNA housekeeping gene. Complete sequences of the gene have been retrieved from the NCBI public database. In the experimental tests the maps show clusters of homologous type strains and present some singular cases potentially due to incorrect classification\ud or erroneous annotations in the database

Publisher: Springer-Verlag
Year: 2007
OAI identifier: oai:centaur.reading.ac.uk:6130

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