Genomic signatures in viral sequences by in-frame and out-frame mutual information

• Published in: Journal of theoretical biology Vol. 403; pp. 1 - 9
• Main Authors: Serrano-Solís, Víctor, Cocho, Germinal, José, Marco V.
• Format: Journal Article
• Language: English
• Published: England Elsevier Ltd 21-08-2016
• Subjects: Algorithms; Archaea; Base Sequence; DNA, Viral - genetics; Eubacteria; Genome, Archaeal - genetics; Genome, Bacterial - genetics; Genome, Viral - genetics; Mutual Information function; Viral space; Virus taxonomy; Viruses - genetics; Mutual Information function; Virus taxonomy; Viral space
• ISSN: 0022-5193; 1095-8541
• DOI: 10.1016/j.jtbi.2016.05.014

In order to understand the unique biology of viruses, we use the Mutual Information Function (MIF) to characterize 792 viral sequences comprising 458 viral whole genomes. A 3-base periodicity (3-bp) was observed only in DNA-viruses whereas RNA-viruses showed irregular patterns. The correlation of MIF values at frequencies of 3-bp (in-frame) with frequencies of 4 and 5bps (out-frame), turned out to be useful to distinguish viruses according to their respective taxonomic order, and whether they pertain to any of the three different kingdoms, Eubacteria, Archaea and Eukarya. The clustering of viruses was carried out by the use of a new statistics, namely, the pair of in- and out-frame values of the MIF. The clustering thus obtained turned out to be entirely consistent with the current viral taxonomy. As a result we were able to compare in a single plot both viral and cellular genomes unlike any given phylogenetic reconstruction.
•Genomic comparison of Viruses, Bacterias and Archaeas through a novel information statistics is presented. The new statistics is used to group viral sequences (single-stranded DNA, double-stranded RNA, and single-stranded RNA viruses), and the results are in agreement with the current viral taxonomy. Bacterial and archaeal genomes are clustered into a separate space.