[en] The fast-growing number of available prokaryotic genomes,
along with their uneven taxonomic distribution, is a prob-
lem when trying to assemble broadly sampled genome sets for
phylogenomics and comparative genomics. Indeed, most of the
new genomes belong to the same subset of hyper-sampled phyla,
such as Proteobacteria and Firmicutes, or even to single species,
such as Escherichia coli (almost 2000 genomes as of Sept 2015),
while the continuous flow of newly discovered phyla prompts for
regular updates. This situation makes it difficult to maintain
sets of representative genomes combining lesser known phyla,
for which only few species are available, and sound subsets of
highly abundant phyla. An automated straightforward method
is required but none are publicly available. The LZ distance, in
conjunction with the quality of the annotations, can be used to
create an automated approach for selecting a subset of represen-
tative genomes without redundancy. We are planning to release
this tool on a website that will be made publicly available.
Research Center/Unit :
CIP - Centre d'Ingénierie des Protéines - ULiège PhytoSYSTEMS - Phylogénomique des eucaryotes
Disciplines :
Biochemistry, biophysics & molecular biology
Author, co-author :
Léonard, Raphaël ; Université de Liège > Département des sciences de la vie > Cristallographie des macromolécules biologiques
Baurain, Denis ; Université de Liège > Département des sciences de la vie > Phylogénomique des eucaryotes
Kerff, Frédéric ; Université de Liège > Département des sciences de la vie > Centre d'ingénierie des protéines
Sauvage, Eric ; Université de Liège > Département des sciences de la vie > Centre d'ingénierie des protéines
Sirjacobs, Damien ; Université de Liège > Département des sciences de la vie > Phylogénomique des eucaryotes
Language :
English
Title :
On the LZ distance for dereplicating redundant prokaryotic genomes
Publication date :
07 December 2015
Number of pages :
A0
Event name :
10th Benelux Bioinformatics Conference
Event organizer :
University of Antwerp
Event place :
Antwerp, Belgium
Event date :
from 7-12-2015 to 8-12-2015
Audience :
International
Funders :
FRIA - Fonds pour la Formation à la Recherche dans l'Industrie et dans l'Agriculture