Genomicus update 2015: KaryoView and MatrixView provide a genome-wide perspective to multispecies comparative genomics.
The Genomicus web server (http://www.genomicus.biologie.ens.fr/genomicus) is a visualization tool allowing comparative genomics in four different phyla (Vertebrate, Fungi, Metazoan and Plants). It provides access to genomic information from extant species, as well as ancestral gene content and gene order for vertebrates and flowering plants. Here we present the new features available for vertebrate genome with a focus on new graphical tools. The interface to enter the database has been improved, two pairwise genome comparison tools are now available (KaryoView and MatrixView) and the multiple genome comparison tools (PhyloView and AlignView) propose three new kinds of representation and a more intuitive menu. These new developments have been implemented for Genomicus portal dedicated to vertebrates. This allows the analysis of 68 extant animal genomes, as well as 58 ancestral reconstructed genomes. The Genomicus server also provides access to ancestral gene orders, to facilitate evolutionary and comparative genomics studies, as well as computationally predicted regulatory interactions, thanks to the representation of conserved non-coding elements with their putative gene targets.
Ecole Normale Supérieure, Institut de Biologie de l'ENS, IBENS, Paris F-75005, France Inserm U1024, Paris F-75005, France CNRS, UMR 8197, Paris F-75005, France alouis@biologie.ens.fr.
Alexandra
A
Louis
Ecole Normale Supérieure, Institut de Biologie de l'ENS, IBENS, Paris F-75005, France Inserm U1024, Paris F-75005, France CNRS, UMR 8197, Paris F-75005, France.
Nga Thi Thuy
NT
Nguyen
European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
Matthieu
M
Muffato
Ecole Normale Supérieure, Institut de Biologie de l'ENS, IBENS, Paris F-75005, France Inserm U1024, Paris F-75005, France CNRS, UMR 8197, Paris F-75005, France.
Hugues
H
Roest Crollius
D000818:Animals; D001483:Base Sequence; D003196:Computer Graphics; D017124:Conserved Sequence; D021901:DNA, Intergenic / Q000737:chemistry; D030541:Databases, Genetic; D019143:Evolution, Molecular; D023061:Gene Order; D016678:Genome; D023281:Genomics; D006801:Humans; D020407:Internet; D010802:Phylogeny; D020539:Sequence Analysis, Protein; D014714:Vertebrates / Q000235:genetics
D021901:DNA, Intergenic