Soft Topographic Map for Clustering and Classification of Bacteria

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

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4 Citazioni (Scopus)

Abstract

In this work a new method for clustering and building atopographic representation of a bacteria taxonomy is presented. Themethod is based on the analysis of stable parts of the genome, theso-called “housekeeping genes”. The proposed method generates topographicmaps of the bacteria taxonomy, where relations among differenttype strains can be visually inspected and verified. Two well knownDNA alignement algorithms are applied to the genomic sequences. Topographicmaps are optimized to represent the similarity among thesequences according to their evolutionary distances. The experimentalanalysis is carried out on 147 type strains of the Gammaprotebacteriaclass by means of the 16S rRNA housekeeping gene. Complete sequencesof the gene have been retrieved from the NCBI public database. In theexperimental tests the maps show clusters of homologous type strainsand present some singular cases potentially due to incorrect classificationor erroneous annotations in the database.
Lingua originaleEnglish
Titolo della pubblicazione ospiteAdvances in Intelligent Data Analysis VII
Pagine332-343
Numero di pagine12
Stato di pubblicazionePublished - 2007

Serie di pubblicazioni

NomeLecture Notes in Computer Science

All Science Journal Classification (ASJC) codes

  • Theoretical Computer Science
  • Computer Science(all)

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