scholarly journals Sequence Classification Using Third-Order Moments

2018 ◽  
Vol 30 (1) ◽  
pp. 216-236
Author(s):  
Rasmus Troelsgaard ◽  
Lars Kai Hansen

Model-based classification of sequence data using a set of hidden Markov models is a well-known technique. The involved score function, which is often based on the class-conditional likelihood, can, however, be computationally demanding, especially for long data sequences. Inspired by recent theoretical advances in spectral learning of hidden Markov models, we propose a score function based on third-order moments. In particular, we propose to use the Kullback-Leibler divergence between theoretical and empirical third-order moments for classification of sequence data with discrete observations. The proposed method provides lower computational complexity at classification time than the usual likelihood-based methods. In order to demonstrate the properties of the proposed method, we perform classification of both simulated data and empirical data from a human activity recognition study.

Viruses ◽  
2019 ◽  
Vol 11 (2) ◽  
pp. 195 ◽  
Author(s):  
Cynthia Maria Chibani ◽  
Anton Farr ◽  
Sandra Klama ◽  
Sascha Dietrich ◽  
Heiko Liesegang

This work reports the method ClassiPhage to classify phage genomes using sequence derived taxonomic features. ClassiPhage uses a set of phage specific Hidden Markov Models (HMMs) generated from clusters of related proteins. The method was validated on all publicly available genomes of phages that are known to infect Vibrionaceae. The phages belong to the well-described phage families of Myoviridae, Podoviridae, Siphoviridae, and Inoviridae. The achieved classification is consistent with the assignments of the International Committee on Taxonomy of Viruses (ICTV), all tested phages were assigned to the corresponding group of the ICTV-database. In addition, 44 out of 58 genomes of Vibrio phages not yet classified could be assigned to a phage family. The remaining 14 genomes may represent phages of new families or subfamilies. Comparative genomics indicates that the ability of the approach to identify and classify phages is correlated to the conserved genomic organization. ClassiPhage classifies phages exclusively based on genome sequence data and can be applied on distinct phage genomes as well as on prophage regions within host genomes. Possible applications include (a) classifying phages from assembled metagenomes; and (b) the identification and classification of integrated prophages and the splitting of phage families into subfamilies.


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