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Soft topographic map for clustering and classification of bacteria

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La Rosa, M., Di Fatta, G., Gaglio, S., Giammanco, G. M., Rizzo, R. and Urso, A. M. (2007) Soft topographic map for clustering and classification of bacteria. In: Berthold, M. R., Shawe-Taylor, J. and Lavrac, N. (eds.) Advances in Intelligent Data Analysis VII : 7th International Symposium on Intelligent Data Analysis, IDA 2007, Ljubljana, Slovenia, September 6-8, 2007. Proceedings. Lecture notes in computer science (4723). Springer-Verlag, Berlin, pp. 332-343. ISBN 9783540748243

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To link to this article DOI: 10.1007/978-3-540-74825-0_30

Abstract/Summary

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.

Item Type:Book or Report Section
Refereed:Yes
Divisions:Faculty of Science > School of Systems Engineering
ID Code:6130
Publisher:Springer-Verlag

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