Computational microbiology in genomic era

Abstract

Microbial genomes and RNA sequences comprise an important part of biological big data. CVTree is a whole-genome based and alignment-free method whereas LVTree is based on alignment of 16S rRNA sequences. They provide two independent ways to construct phylogenetic trees and to extract taxonomic information for prokaryotes. The automation of these two approaches make the study of prokaryotic phylogeny and classification by-product of big data analysis and come as a rescue to the declining discipline of taxonomy. Especially, the whole-genome based CVTree not only provides a tool for large-scale study but also possesses high resolution power at the species level and below, a distinctive feature beyond the reach of 16S rRNA sequence analysis. These methods taken together may open new directions in microbiological research. This paper is a brief review of our recent work.