GEnView: a gene-centric, phylogeny-based comparative genomics pipeline for bacterial genomes and plasmids
Artikel i vetenskaplig tidskrift, 2021

Comparing genomic loci of a given bacterial gene across strains and species can provide insights into their evolution, including information on e.g. acquired mobility, the degree of conservation between different taxa or indications of horizontal gene transfer events. While thousands of bacterial genomes are available to date, there is no software that facilitates comparisons of individual gene loci for a large number of genomes. GEnView (Genetic Environment View) is a Python-based pipeline for the comparative analysis of gene-loci in a large number of bacterial genomes, providing users with automated, taxon-selective access to the >800.000 genomes and plasmids currently available in the NCBI Assembly and RefSeq databases, and is able to process local genomes that are not deposited at NCBI, enabling searches for genomic sequences and to analyze their genetic environments through the interactive visualization and extensive metadata files created by GEnView.

Författare

Stefan Ebmeyer

Göteborgs universitet

Roelof Dirk Coertze

Göteborgs universitet

Fanny Berglund

Chalmers, Matematiska vetenskaper, Tillämpad matematik och statistik

Göteborgs universitet

Erik Kristiansson

Chalmers, Matematiska vetenskaper, Tillämpad matematik och statistik

Göteborgs universitet

D. G. Joakim Larsson

Göteborgs universitet

Bioinformatics

1367-4803 (ISSN) 1367-4811 (eISSN)

btab855

Ämneskategorier

Bioinformatik och systembiologi

Genetik

DOI

10.1093/bioinformatics/btab855

PubMed

34951622

Mer information

Senast uppdaterat

2022-02-24