Search results for "Genomic Sequence Clustering"
showing 2 items of 2 documents
Comparison of genomic sequences clustering using Normalized Compression Distance and Evolutionary Distance
2008
Genomic sequences are usually compared using evolutionary distance, a procedure that implies the alignment of the sequences. Alignment of long sequences is a long procedure and the obtained dissimilarity results is not a metric. Recently the normalized compression distance was introduced as a method to calculate the distance between two generic digital objects, and it seems a suitable way to compare genomic strings. In this paper the clustering and the mapping, obtained using a SOM, with the traditional evolutionary distance and the compression distance are compared in order to understand if the two distances sets are similar. The first results indicate that the two distances catch differen…
Soft Topographic Map for Clustering and Classification of Bacteria
2007
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…