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Compression-based classification of biological sequences and structures via the Universal Similarity Metric: experimental assessment

Author
Ferragina, P.; Giancarlo, R.; Greco, V.; Manzini, Giovanni; Valiente, G.
Type of activity
Journal article
Journal
BMC bioinformatics
Date of publication
2007-07
Volume
8
Number
252
First page
1
Last page
20
DOI
https://doi.org/10.1186/1471-2105-8-252 Open in new window
Repository
http://hdl.handle.net/2117/113030 Open in new window
URL
https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-8-252 Open in new window
Abstract
Similarity of sequences is a key mathematical notion for Classification and Phylogenetic studies in Biology. It is currently primarily handled using alignments. However, the alignment methods seem inadequate for post-genomic studies since they do not scale well with data set size and they seem to be confined only to genomic and proteomic sequences. Therefore, alignment-free similarity measures are actively pursued. Among those, USM (Universal Similarity Metric) has gained prominence. It is based...
Citation
Ferragina, P., Giancarlo, R., Greco, V., Manzini, Giovanni, Valiente, G. Compression-based classification of biological sequences and structures via the Universal Similarity Metric: experimental assessment. "BMC bioinformatics", Juliol 2007, vol. 8, núm. 252, p. 1-20.
Keywords
CD, Compression dissimilarity, NCD, Normalized compression sissimilarity, UCD, USM, Universal compression dissimilarity, Universal similarity metric
Group of research
ALBCOM - Algorithms, Computational Biology, Complexity and Formal Methods

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