Magnus representation of genome sequences. (7th November 2019)

• Record Type: Journal Article
• Authors: Wu, Chengyuan; Ren, Shiquan; Wu, Jie; Xia, Kelin
• Is Part Of: Journal of theoretical biology. Volume 480(2019)
• Page Start: 104
• Page End: 111
• Publication Date: 2019-11-07
• Subjects: Alignment-free -- Genome sequence -- Sequence analysis -- Ebolavirus; Biology -- Periodicals; Biological Science Disciplines -- Periodicals; Biology -- Periodicals; Biologie -- Périodiques; Theoretische biologie; Biology; Periodicals; 571.05
• DOI: 10.1016/j.jtbi.2019.08.004
• Languages: English
• ISSNs: 0022-5193

Abstract

Highlights: We introduce an alignment-free method, the Magnus Representation, to analyze genome sequences. The Magnus Representation captures higher-order information in genome sequences. We combine our approach with the idea of k-mers to define an effectively computable Mean Magnus Vector. We perform phylogenetic analysis on three datasets: mosquito-borne viruses, filoviruses, and bacterial genomes. Abstract: We introduce an alignment-free method, the Magnus Representation, to analyze genome sequences. The Magnus Representation captures higher-order information in genome sequences. We combine our approach with the idea of k -mers to define an effectively computable Mean Magnus Vector. We perform phylogenetic analysis on three datasets: mosquito-borne viruses, filoviruses, and bacterial genomes. Our results on ebolaviruses are consistent with previous phylogenetic analyses, and confirm the modern viewpoint that the 2014 West African Ebola outbreak likely originated from Central Africa. Our analysis also confirms the close relationship between Bundibugyo ebolavirus and Taï Forest ebolavirus . For bacterial genomes, our method is able to classify relatively well at the family and genus level, as well as at higher levels such as phylum level. The bacterial genomes are also separated well into Gram-positive and Gram-negative subgroups.