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. 2008 Jan;36(Database issue):D267-70.
doi: 10.1093/nar/gkm852. Epub 2007 Oct 11.

OPTIC: orthologous and paralogous transcripts in clades

Andreas Heger  1 , Chris P Ponting
Affiliations

OPTIC: orthologous and paralogous transcripts in clades

Andreas Heger et al. Nucleic Acids Res. 2008 Jan.

Abstract

The genome sequences of a large number of metazoan species are now known. As multiple closely related genomes are sequenced, comparative studies that previously focussed on only pairs of genomes can now be extended over whole clades. The orthologous and paralogous transcripts in clades (OPTIC) database currently provides sets of gene predictions and orthology assignments for three clades: (i) amniotes, including human, dog, mouse, opossum, platypus and chicken (17 443 orthologous groups); (ii) a Drosophila clade of 12 species (12 889 orthologous groups) and (iii) a nematode clade of four species (13 626 orthologous groups). Gene predictions, multiple alignments and phylogenetic trees are freely available to browse and download from http://genserv.anat.ox.ac.uk/clades. Further genomes and clades will be added in the future.

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Figures

Figure 1.
Figure 1.
Browsing the orthology database. A sample session starts with a query for all simple 1:1 ortholog sets (bottom left). It continues with a list of all simple 1:1 ortholog sets containing all six species from the amniotic clade, then by a selection of one particular ortholog set (number 114), and finally with a viewing of the gene-based multiple sequence alignment.
See this image and copyright information in PMC

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