Limits...
Genomicus update 2015: KaryoView and MatrixView provide a genome-wide perspective to multispecies comparative genomics.

Louis A, Nguyen NT, Muffato M, Roest Crollius H - Nucleic Acids Res. (2014)

Bottom Line: 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.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.

View Article: PubMed Central - PubMed

Affiliation: 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.

Show MeSH
PhyloView example centered on the SPA17 gene of human. (A) Default view of PhyloView in the schematic scale. The SPA17 gene (reference gene) and all its homologs are centered on the middle line. The thick blue line in the specie tree leads the root ancestor to the reference species (Homo sapiens) and other species. One can switch between the default view (based on gene tree membership) and representation of similarity score between proteins of the same family (B) or dN/dS ratio comparisons (C). Those two alternative representations highlight that despite the fact that SPA17 shares a very high similarity score (almost 100% of identity) to all its orthologs, selection patterns are widely different (as suggested by dN/dS).
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4383929&req=5

Figure 3: PhyloView example centered on the SPA17 gene of human. (A) Default view of PhyloView in the schematic scale. The SPA17 gene (reference gene) and all its homologs are centered on the middle line. The thick blue line in the specie tree leads the root ancestor to the reference species (Homo sapiens) and other species. One can switch between the default view (based on gene tree membership) and representation of similarity score between proteins of the same family (B) or dN/dS ratio comparisons (C). Those two alternative representations highlight that despite the fact that SPA17 shares a very high similarity score (almost 100% of identity) to all its orthologs, selection patterns are widely different (as suggested by dN/dS).

Mentions: The second new feature (Figure 3), available in both PhyloView and AlignView, is the ability to use the colors of genes to represent the percentage of sequence identity between homologs of the reference genome instead of orthology (Figure 3B). A second new option is to show the dN/dS ratio computed from multiple alignments of coding sequences from genes of the same family (Figure 3C).


Genomicus update 2015: KaryoView and MatrixView provide a genome-wide perspective to multispecies comparative genomics.

Louis A, Nguyen NT, Muffato M, Roest Crollius H - Nucleic Acids Res. (2014)

PhyloView example centered on the SPA17 gene of human. (A) Default view of PhyloView in the schematic scale. The SPA17 gene (reference gene) and all its homologs are centered on the middle line. The thick blue line in the specie tree leads the root ancestor to the reference species (Homo sapiens) and other species. One can switch between the default view (based on gene tree membership) and representation of similarity score between proteins of the same family (B) or dN/dS ratio comparisons (C). Those two alternative representations highlight that despite the fact that SPA17 shares a very high similarity score (almost 100% of identity) to all its orthologs, selection patterns are widely different (as suggested by dN/dS).
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4383929&req=5

Figure 3: PhyloView example centered on the SPA17 gene of human. (A) Default view of PhyloView in the schematic scale. The SPA17 gene (reference gene) and all its homologs are centered on the middle line. The thick blue line in the specie tree leads the root ancestor to the reference species (Homo sapiens) and other species. One can switch between the default view (based on gene tree membership) and representation of similarity score between proteins of the same family (B) or dN/dS ratio comparisons (C). Those two alternative representations highlight that despite the fact that SPA17 shares a very high similarity score (almost 100% of identity) to all its orthologs, selection patterns are widely different (as suggested by dN/dS).
Mentions: The second new feature (Figure 3), available in both PhyloView and AlignView, is the ability to use the colors of genes to represent the percentage of sequence identity between homologs of the reference genome instead of orthology (Figure 3B). A second new option is to show the dN/dS ratio computed from multiple alignments of coding sequences from genes of the same family (Figure 3C).

Bottom Line: 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.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.

View Article: PubMed Central - PubMed

Affiliation: 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.

Show MeSH