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 present some singular cases potentially due to incorrect classification
or erroneous annotations in the database.
title = "Soft Topographic Map for Clustering and Classification of Bacteria",
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 present some singular cases potentially due to incorrect classification or erroneous annotations in the database.",
author = "{Di Fatta, G.; Rizzo, R.} and Salvatore Gaglio and Alberto Urso and Giovanni Giammanco and {La Rosa}, Massimo",
year = "2007",
language = "English",
}
TY - CONF
T1 - Soft Topographic Map for Clustering and Classification of Bacteria
AU - Di Fatta, G.; Rizzo, R.
AU - Gaglio, Salvatore
AU - Urso, Alberto
AU - Giammanco, Giovanni
AU - La Rosa, Massimo
PY - 2007
Y1 - 2007
N2 - 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 present some singular cases potentially due to incorrect classification
or erroneous annotations in the database.
AB - 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 present some singular cases potentially due to incorrect classification
or erroneous annotations in the database.