Topographic maps for clustering and fast identification of bacteria using 16s housekeeping gene

Salvatore Gaglio, Massimo La Rosa, Riccardo Rizzoy, Alfonso Ursoz, Salvatore Gagliox

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Abstract

In microbial identification the standard method to attribute a specific name to abacterial isolate relays on the comparison of morphologic and phenotypic charactersto those described for type or typical strains. In the last years a new standard foridentifying bacteria using genotypic information began to be developed. In this newapproach phylogenetic relationships of bacteria could be determined by comparing astable part of the bacteria genetic code, the so called “housekeeping genes”. The mostcommonly used gene for taxonomic purposes for bacteria is the 16S rRNA. The goalof this chapter is to show that genotypic features can be used to build a topographicmap for clustering of a large set of bacteria. The map allows to visually inspect therelative distances among sequences of different orders or classes. Moreover it canbe used for fast identification of suspect sequences of bacteria, using a small set ofsequences prototypes.
Lingua originaleEnglish
Titolo della pubblicazione ospiteComputational Intelligence
Numero di pagine18
Stato di pubblicazionePublished - 2012

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All Science Journal Classification (ASJC) codes

  • Computational Mathematics
  • Artificial Intelligence

Cita questo

Gaglio, S., Rosa, M. L., Rizzoy, R., Ursoz, A., & Gagliox, S. (2012). Topographic maps for clustering and fast identification of bacteria using 16s housekeeping gene. In Computational Intelligence