title: eggNOG v2.0: extending the evolutionary genealogy of genes with enhanced non-supervised orthologous groups, species and functional annotations.
abstract: The identification of orthologous relationships forms the basis for most comparative genomics studies. Here, we present the second version of the eggNOG database, which contains orthologous groups (OGs) constructed through identification of reciprocal best BLAST matches and triangular linkage clustering. We applied this procedure to 630 complete genomes (529 bacteria, 46 archaea and 55 eukaryotes), which is a 2-fold increase relative to the previous version. The pipeline yielded 224,847 OGs, including 9724 extended versions of the original COG and KOG. We computed OGs for different levels of the tree of life; in addition to the species groups included in our first release (i.e. fungi, metazoa, insects, vertebrates and mammals), we have now constructed OGs for archaea, fishes, rodents and primates. We automatically annotate the non-supervised orthologous groups (NOGs) with functional descriptions, protein domains, and functional categories as defined initially for the COG/KOG database. In-depth analysis is facilitated by precomputed high-quality multiple sequence alignments and maximum-likelihood trees for each of the available OGs. Altogether, eggNOG covers 2,242 035 proteins (built from 2,590,259 proteins) and provides a broad functional description for at least 1,966,709 (88%) of them. Users can access the complete set of orthologous groups via a web interface at: http://eggnog.embl.de.
authors.affiliation: European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany.
authors.forename: J
authors.initials: J
authors.lastname: Muller
authors.forename: D
authors.initials: D
authors.lastname: Szklarczyk
authors.forename: P
authors.initials: P
authors.lastname: Julien
authors.forename: I
authors.initials: I
authors.lastname: Letunic
authors.forename: A
authors.initials: A
authors.lastname: Roth
authors.forename: M
authors.initials: M
authors.lastname: Kuhn
authors.forename: S
authors.initials: S
authors.lastname: Powell
authors.forename: C
authors.initials: C
authors.lastname: von Mering
authors.forename: T
authors.initials: T
authors.lastname: Doerks
authors.forename: L J
authors.initials: LJ
authors.lastname: Jensen
authors.forename: P
authors.initials: P
authors.lastname: Bork
mesh_terms: D020816:Amino Acid Motifs / Q000235:genetics*; D000818:Animals; D001105:Archaea; D019295:Computational Biology / Q000379:methods* / Q000639:trends; D030541:Databases, Genetic; D030561:Databases, Nucleic Acid; D030562:Databases, Protein; D005399:Fishes; D016680:Genome, Bacterial; D006801:Humans; D016247:Information Storage and Retrieval / Q000379:methods; D020407:Internet; D011323:Primates; D017434:Protein Structure, Tertiary; D051381:Rats; D012984:Software