soft topographic maps for clustering and classifying bacteria using housekeeping genes软地形图使用管家基因进行聚类和分类细菌.pdfVIP

Hindawi Publishing Corporation Advances in Artificial Neural Systems Volume 2011, Article ID 617427, 8 pages doi:10.1155/2011/617427 Research Article Soft Topographic Maps for Clustering and Classifying Bacteria Using Housekeeping Genes Massimo La Rosa, Riccardo Rizzo, and Alfonso Urso ICAR-CNR, Consiglio Nazionale delle Ricerche, Viale delle Scienze, Ed.11, 90128 Palermo, Italy Correspondence should be addressed to Riccardo Rizzo, ricrizzo@r.it Received 11 May 2011; Revised 13 July 2011; Accepted 26 July 2011 Academic Editor: Tomasz G. Smolinski Copyright © 2011 Massimo La Rosa et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. The Self-Organizing Map (SOM) algorithm is widely used for building topographic maps of data represented in a vectorial space, but it does not operate with dissimilarity data. Soft Topographic Map (STM) algorithm is an extension of SOM to arbitrary distance measures, and it creates a map using a set of units, organized in a rectangular lattice, defining data neighbourhood relationships. In the last years, a new standard for identifying bacteria using genotypic information began to be developed. In this new approach, phylogenetic relationships of bacteria could be determined by comparing a stable part of the bacteria genetic code, the so-called “housekeeping genes.” The goal of this work is to build a topographic representation of bacteria clusters, by means of self-organizing maps, starting from genotypic features regarding housekeeping genes. 1. Introduction nucleotide sequences is not reliable and well structured, t