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.
Lingua originale | English |
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Stato di pubblicazione | Published - 2007 |
All Science Journal Classification (ASJC) codes
- Theoretical Computer Science
- Computer Science(all)