Limits...
The OMA orthology database in 2015: function predictions, better plant support, synteny view and other improvements.

Altenhoff AM, Škunca N, Glover N, Train CM, Sueki A, Piližota I, Gori K, Tomiczek B, Müller S, Redestig H, Gonnet GH, Dessimoz C - Nucleic Acids Res. (2014)

Bottom Line: The Orthologous Matrix (OMA) project is a method and associated database inferring evolutionary relationships amongst currently 1706 complete proteomes (i.e. the protein sequence associated for every protein-coding gene in all genomes).In this update article, we present six major new developments in OMA: (i) a new web interface; (ii) Gene Ontology function predictions as part of the OMA pipeline; (iii) better support for plant genomes and in particular homeologs in the wheat genome; (iv) a new synteny viewer providing the genomic context of orthologs; (v) statically computed hierarchical orthologous groups subsets downloadable in OrthoXML format; and (vi) possibility to export parts of the all-against-all computations and to combine them with custom data for 'client-side' orthology prediction.OMA can be accessed through the OMA Browser and various programmatic interfaces at http://omabrowser.org.

View Article: PubMed Central - PubMed

Affiliation: University College London, Gower Street, London WC1E 6BT, UK Swiss Institute of Bioinformatics, Universitätstr. 6, 8092 Zurich, Switzerland ETH Zurich, Computer Science, Universitätstr. 6, 8092 Zurich, Switzerland.

Show MeSH

Related in: MedlinePlus

Screenshot of the new OMA synteny viewer with the ADH1A gene in human (Gene ID 22168) as query. Each gene is illustrated as a box containing a numerical OMA Gene ID and an arrow to indicate the gene's orientation. The colour of genes outside the query species indicates orthologous relationship with human genes, with bands of colour capturing many-to-one and many-to-many relationships. Genes that are non-orthologous to all nine human genes contained in this window are displayed in grey. The fragmented assemblies of tarsier (TARSY) and mouse lemur (MICMU) contain no genes next to 03287 and 02276, respectively.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4383958&req=5

Figure 5: Screenshot of the new OMA synteny viewer with the ADH1A gene in human (Gene ID 22168) as query. Each gene is illustrated as a box containing a numerical OMA Gene ID and an arrow to indicate the gene's orientation. The colour of genes outside the query species indicates orthologous relationship with human genes, with bands of colour capturing many-to-one and many-to-many relationships. Genes that are non-orthologous to all nine human genes contained in this window are displayed in grey. The fragmented assemblies of tarsier (TARSY) and mouse lemur (MICMU) contain no genes next to 03287 and 02276, respectively.

Mentions: To illustrate the usefulness of the new synteny viewer, consider the arrangement of alcohol dehydrogenase (ADH) genes around human ADH1A (Figure 5). The human ADH gene cluster ADH7 (class IV)-ADH1C (class I)-ADH1B (class I)-ADH1A (class I)-ADH6 (class V)-ADH4 (class II)-ADH5 (class III) is displayed in the first row. Because the cluster sits on the complementary strand, it appears in reverse order—starting in column 3 (Gene ID 22172) and ending in column −3 (22163). The synteny viewer suggests that the neighbourhood of orthologous genes is well conserved amongst simians, but the conservation diminishes as we move to more distant lineages. Genes with stripes are in one-to-many or many-to-many orthologous relationships with human ADH1A (22168), human ADH1B (22169) and human ADH1C (22171). In particular, the presence of two orthologs in the bushbaby (OTOGA) suggests a separate duplication within the lemur lineage, yielding many-to-many orthology. These observations are all consistent with detailed analyses in the literature (42). Although positioned within well-conserved syntenic regions, genes 13367 in the chimp (PANTR) and 15069 in the gorilla (GORGO) have no human orthologous counterpart in this region. On account of their very short lengths—13 AA and 14 AA, respectively—they are likely to be fragments. Furthermore, the absence of flanking genes in the tarsier (TARSY) and mouse lemur (MICMU) is due to the low quality of the genome assembly in these regions.


The OMA orthology database in 2015: function predictions, better plant support, synteny view and other improvements.

Altenhoff AM, Škunca N, Glover N, Train CM, Sueki A, Piližota I, Gori K, Tomiczek B, Müller S, Redestig H, Gonnet GH, Dessimoz C - Nucleic Acids Res. (2014)

Screenshot of the new OMA synteny viewer with the ADH1A gene in human (Gene ID 22168) as query. Each gene is illustrated as a box containing a numerical OMA Gene ID and an arrow to indicate the gene's orientation. The colour of genes outside the query species indicates orthologous relationship with human genes, with bands of colour capturing many-to-one and many-to-many relationships. Genes that are non-orthologous to all nine human genes contained in this window are displayed in grey. The fragmented assemblies of tarsier (TARSY) and mouse lemur (MICMU) contain no genes next to 03287 and 02276, respectively.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4383958&req=5

Figure 5: Screenshot of the new OMA synteny viewer with the ADH1A gene in human (Gene ID 22168) as query. Each gene is illustrated as a box containing a numerical OMA Gene ID and an arrow to indicate the gene's orientation. The colour of genes outside the query species indicates orthologous relationship with human genes, with bands of colour capturing many-to-one and many-to-many relationships. Genes that are non-orthologous to all nine human genes contained in this window are displayed in grey. The fragmented assemblies of tarsier (TARSY) and mouse lemur (MICMU) contain no genes next to 03287 and 02276, respectively.
Mentions: To illustrate the usefulness of the new synteny viewer, consider the arrangement of alcohol dehydrogenase (ADH) genes around human ADH1A (Figure 5). The human ADH gene cluster ADH7 (class IV)-ADH1C (class I)-ADH1B (class I)-ADH1A (class I)-ADH6 (class V)-ADH4 (class II)-ADH5 (class III) is displayed in the first row. Because the cluster sits on the complementary strand, it appears in reverse order—starting in column 3 (Gene ID 22172) and ending in column −3 (22163). The synteny viewer suggests that the neighbourhood of orthologous genes is well conserved amongst simians, but the conservation diminishes as we move to more distant lineages. Genes with stripes are in one-to-many or many-to-many orthologous relationships with human ADH1A (22168), human ADH1B (22169) and human ADH1C (22171). In particular, the presence of two orthologs in the bushbaby (OTOGA) suggests a separate duplication within the lemur lineage, yielding many-to-many orthology. These observations are all consistent with detailed analyses in the literature (42). Although positioned within well-conserved syntenic regions, genes 13367 in the chimp (PANTR) and 15069 in the gorilla (GORGO) have no human orthologous counterpart in this region. On account of their very short lengths—13 AA and 14 AA, respectively—they are likely to be fragments. Furthermore, the absence of flanking genes in the tarsier (TARSY) and mouse lemur (MICMU) is due to the low quality of the genome assembly in these regions.

Bottom Line: The Orthologous Matrix (OMA) project is a method and associated database inferring evolutionary relationships amongst currently 1706 complete proteomes (i.e. the protein sequence associated for every protein-coding gene in all genomes).In this update article, we present six major new developments in OMA: (i) a new web interface; (ii) Gene Ontology function predictions as part of the OMA pipeline; (iii) better support for plant genomes and in particular homeologs in the wheat genome; (iv) a new synteny viewer providing the genomic context of orthologs; (v) statically computed hierarchical orthologous groups subsets downloadable in OrthoXML format; and (vi) possibility to export parts of the all-against-all computations and to combine them with custom data for 'client-side' orthology prediction.OMA can be accessed through the OMA Browser and various programmatic interfaces at http://omabrowser.org.

View Article: PubMed Central - PubMed

Affiliation: University College London, Gower Street, London WC1E 6BT, UK Swiss Institute of Bioinformatics, Universitätstr. 6, 8092 Zurich, Switzerland ETH Zurich, Computer Science, Universitätstr. 6, 8092 Zurich, Switzerland.

Show MeSH
Related in: MedlinePlus