2008, Nucleic Acids Research, eggNOG: automated construction and annotation of orthologous groups of genes

eggNOG: automated construction and annotation
of orthologous groups of genes

Lars Juhl Jensen1, Philippe Julien1, Michael Kuhn1, Christian von Mering2,
Jean Muller1, Tobias Doerks1 and Peer Bork1,3,*
1European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany, 2University of Zurich
and Swiss Institute of Bioinformatics, Winterthurerstrasse 190, 8057 Zurich, Switzerland and 3Max-Delbru¨ ck-
Centre for Molecular Medicine, Robert-Ro¨ ssle-Strrasse 10, 13092 Berlin, Germany

ABSTRACT
The identification of orthologous genes forms the
basis for most comparative genomics studies.
Existing approaches either lack functional annotation
of the identified orthologous groups, hampering
the interpretation of subsequent results, or are
manually annotated and thus lag behind the rapid
sequencing of new genomes. Here we present
the eggNOG database (‘evolutionary genealogy of
genes: Non-supervised Orthologous Groups’),
which contains orthologous groups constructed
from Smith–Waterman alignments through identification
of reciprocal best matches and triangular
linkage clustering. Applying this procedure to 312
bacterial, 26 archaeal and 35 eukaryotic genomes
yielded 43 582 course-grained orthologous groups
of which 9724 are extended versions of those
from the original COG/KOG database. We also
constructed more fine-grained groups for selected
subsets of organisms, such as the 19 914 mammalian
orthologous groups. We automatically
annotated our non-supervised orthologous groups
with functional descriptions, which were derived by
identifying common denominators for the genes
based on their individual textual descriptions,
annotated functional categories, and predicted
protein domains. The orthologous groups in
eggNOG contain 1 241 751 genes and provide at
least a broad functional description for 77% of them.
Users can query the resource for individual genes
via a web interface or download the complete set
of orthologous groups at http://eggnog.embl.de.