Genomicus in 2022: comparative tools for thousands of genomes and reconstructed ancestors

Nga thi thuy Nguyen (1) , Pierre Vincens (2, 1) , Jean François Dufayard (3, 4) , Hugues Roest crollius (5) , Alexandra Louis (5)

1 IBENS - Institut de biologie de l'ENS Paris
2 Modélisation mathématique et statistique en biologie et médecine
3 UMR AGAP - Amélioration génétique et adaptation des plantes méditerranéennes et tropicales
4 Cirad-BIOS - Département Systèmes Biologiques
5 DYOGEN - DYnamique et Organisation des GENomes - Equipe de l'IBENS

Genomicus is a database and web-server dedicated to comparative genomics in eukaryotes. Its main functionality is to graphically represent the conservation of genomic blocks between multiple genomes, locally around a specific gene of interest or genome-wide through karyotype comparisons. Since 2010 and its first release, Genomicus has synchronized with 60 Ensembl releases and seen the addition of functions that have expanded the type of analyses that users can perform. Today, five public instances of Genomicus are supporting a total number of 1029 extant genomes and 621 ancestral reconstructions from all eukaryotes kingdoms available in Ensembl and Ensembl Genomes databases complemented with four additional instances specific to taxonomic groups of interest. New visualization and query tools are described in this manuscript. Genomicus is freely available at http://www.genomicus.bio.ens.psl.eu/genomicus.

Domaines: Bio-Informatique, Biologie Systémique [q-bio.QM]; Génomique, Transcriptomique et Protéomique [q-bio.GN]

Nga thi thuy Nguyen, Pierre Vincens, Jean François Dufayard, Hugues Roest crollius, Alexandra Louis. Genomicus in 2022: comparative tools for thousands of genomes and reconstructed ancestors. Nucleic Acids Research, 2022, 50 (D1), pp.D1025-D1031. ⟨10.1093/nar/gkab1091⟩. ⟨hal-03438462⟩