For instance, to introduce a cross-reference to UniProt or RefSeq, we have required both exact species and exact sequence matching. Until now, we have adopted stringent requirements to establish cross-references. The second way pertains to the mapping criteria. First, we now provide cross-references to additional resources, including STRING ( 18), Bgee ( 17) and Swiss-Model ( 19). We have extended our cross-references in two ways. Cross-references to other resources are thus critical. Furthermore, many OMA users also combine OMA orthologs with other resources. Conversely, OMA orthologs are integrated by various resources, including UniProt, HGNC/VGNC, GenBank ( 15), the Alliance of Genome Resources ( 16), and Bgee ( 17). We import genomic and functional data from various different sources, notably Ensembl ( 10), UniProt ( 11), RefSeq ( 12), Gene3D ( 13) and HGNC/VGNC ( 14). The OMA Browser is part of a rich ecosystem of bioinformatic resources. The query takes as an input the identifier of the gene, and outputs all isoforms, including their identifiers and genomic coordinates, and specifies which isoform was selected as reference. This change will roll out as we update and add new genomes to OMA.Īdditionally, isoform data is now available through the programmatic access (REST API), under the protein section. Second, starting from now, we will include in the Browser all isoforms annotated in the input genomes, even those which we do not consider as candidate isoforms in the all-against-all computations (to save computations, we disregard isoforms which are covered by candidate isoforms in at least 90% of their length). First, we list all isoforms in a table accessible from the gene-centric view, with lengths, exon structure and indication of the reference isoform selected by OMA. While this reference isoform procedure has been part of the OMA algorithm since its inception, we have improved our reporting of isoforms in the Browser. Interestingly, in the current release, the reference isoform selected by OMA is not the longest one for 48.6% of all genes with more than one isoform. By contrast, OMA keeps multiple candidate isoforms for the all-against-all alignment phase, and selects as reference the isoform which has the best matches across all species-which can be thought of as the most evolutionarily conserved isoform. Most orthology resources select a priori one reference (‘canonical’) isoform to be used for orthology inference, usually the longest one. Either group type provides a list of members and the ability to look for closely related groups.įinally, genome-centric pages, recognisable by their red theme, provide information on the underlying species, a list of all genes associated with them, a list of closely related genomes in OMA, and access to the pairwise global synteny viewer introduced earlier ( 6).Įukaryotic species, especially vertebrates, use alternative splicing, by which a diversity of protein sequences can originate from a single gene by varying combinations of its exons ( 9). More details on the differences between OMA Groups and HOGs and their uses are provided in the primer ( 8). Group-centric pages, recognisable by their dark blue theme, are of two subtypes: OMA groups, which are groups in which every gene is orthologous to every other one, and HOGs, which provide a formal way of defining families and subfamilies, and provide a model of the proteomes of ancestral genomes. Another novelty is the table of pairwise paralogs, which are derived from the HOGs only (since neither pairwise comparison nor OMA groups reliably induce paralogy). Using the side menu, users can filter the list to particular lines of evidence, or particular taxonomic clades. More details on the various types of pairwise orthologs are provided in a recent primer ( 8). The table of orthologs has been improved to include the evidence supporting each prediction: the browser reports whether a particular pair is predicted to be orthologous based on pairwise analyses, by virtue of being in the same OMA group, and/or by being in the same Hierarchical Orthologous Group (HOGs-nested groups of genes which have descended from a common ancestral gene in a given clade of species). Gene-centric pages, recognisable by their light blue colour theme, provide information with respect to a particular gene, including sequence, cross references, functional annotations, as well as evolutionary information. New OMA Browser website, with a new landing page ( A), and the database part organised in genes ( B), groups ( C) and genomes ( D).
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