Soft topographic map for clustering and classification of bacteria

Authors:
Massimo La Rosa;Giuseppe Di Fatta;Salvatore Gaglio;Giovanni M. Giammanco;Riccardo Rizzo;Alfonso M. Urso
Affiliations:
ICAR, Consiglio Nazionale delle Ricerche, Palermo, Italy;School of Systems Engineering, University of Reading, UK;ICAR, Consiglio Nazionale delle Ricerche, Palermo, Italy and Dipartimento di Ingegneria Informatica, Universitá di Palermo, Italy;Dipartimento di Igiene e Microbiologia, Universitá di Palermo, Italy;ICAR, Consiglio Nazionale delle Ricerche, Palermo, Italy;ICAR, Consiglio Nazionale delle Ricerche, Palermo, Italy
Venue:
IDA'07 Proceedings of the 7th international conference on Intelligent data analysis
Year:
2007

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Abstract

In this work a new method for clustering and building a 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 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 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 presents some singular cases potentially due to incorrect classification or erroneous annotations in the database.