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Nucleic Acids Research Advance Access published online on October 11, 2007
Nucleic Acids Research, doi:10.1093/nar/gkm852
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© 2007 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Database Issue

OPTIC: orthologous and paralogous transcripts in clades

Andreas Heger* and Chris P. Ponting

Department of Physiology, Anatomy and Genetics, MRC Functional Genetics Unit, University of Oxford, Le Gros Clark Building, Oxford OX1 3QX, UK

* To whom correspondence should be addressed. Tel: +44 1865 2 85 85 4; Fax: +44 1865 2 85 86 2; Email: andreas.heger{at}dpag.ox.ac.uk

Correspondence may also be addressed to Chris Ponting. Tel: +44 1865 2 85 85 5; Fax: +44 1865 2 85 86 2; Email: chris.ponting{at}dpag.ox.ac.uk

Received August 13, 2007. Revised September 25, 2007. Accepted September 26, 2007.

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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