eggNOG v3.0: Orthologous groups covering 1133 organisms at 41 different taxonomic ranges

TY - JOUR

T1 - eggNOG v3.0

T2 - Orthologous groups covering 1133 organisms at 41 different taxonomic ranges

AU - Powell, S.

AU - Trachana, K.

AU - Letunic, I.

AU - Doerks, T.

AU - Bork, P.

AU - Szklarczyk, D.

AU - Jensen, L.J.

AU - Roth, A.

AU - Von Mering, C.

AU - Kuhn, M.

AU - Muller, J.

AU - Arnold, R.

AU - Rattei, T.

PY - 2012/1

Y1 - 2012/1

N2 - Orthologous relationships form the basis of most comparative genomic and metagenomic studies and are essential for proper phylogenetic and functional analyses. The third version of the eggNOG database (http://eggnog.embl.de) contains non-supervised orthologous groups constructed from 1133 organisms, doubling the number of genes with orthology assignment compared to eggNOG v2. The new release is the result of a number of improvements and expansions: (i) the underlying homology searches are now based on the SIMAP database; (ii) the orthologous groups have been extended to 41 levels of selected taxonomic ranges enabling much more fine-grained orthology assignments; and (iii) the newly designed web page is considerably faster with more functionality. In total, eggNOG v3 contains 721,801 orthologous groups, encompassing a total of 4,396,591 genes. Additionally, we updated 4873 and 4850 original COGs and KOGs, respectively, to include all 1133 organisms. At the universal level, covering all three domains of life, 101,208 orthologous groups are available, while the others are applicable at 40 more limited taxonomic ranges. Each group is amended by multiple sequence alignments and maximum-likelihood trees and broad functional descriptions are provided for 450,904 orthologous groups (62.5%).

AB - Orthologous relationships form the basis of most comparative genomic and metagenomic studies and are essential for proper phylogenetic and functional analyses. The third version of the eggNOG database (http://eggnog.embl.de) contains non-supervised orthologous groups constructed from 1133 organisms, doubling the number of genes with orthology assignment compared to eggNOG v2. The new release is the result of a number of improvements and expansions: (i) the underlying homology searches are now based on the SIMAP database; (ii) the orthologous groups have been extended to 41 levels of selected taxonomic ranges enabling much more fine-grained orthology assignments; and (iii) the newly designed web page is considerably faster with more functionality. In total, eggNOG v3 contains 721,801 orthologous groups, encompassing a total of 4,396,591 genes. Additionally, we updated 4873 and 4850 original COGs and KOGs, respectively, to include all 1133 organisms. At the universal level, covering all three domains of life, 101,208 orthologous groups are available, while the others are applicable at 40 more limited taxonomic ranges. Each group is amended by multiple sequence alignments and maximum-likelihood trees and broad functional descriptions are provided for 450,904 orthologous groups (62.5%).

KW - Databases, Genetic

KW - Genomics

KW - Phylogeny

KW - Proteins

KW - Sequence Homology

KW - User-Computer Interface

UR - http://www.scopus.com/inward/record.url?scp=84861203603&partnerID=8YFLogxK

U2 - 10.1093/nar/gkr1060

DO - 10.1093/nar/gkr1060

M3 - Journal article

C2 - 22096231

SN - 0305-1048

VL - 40

SP - D284-9

JO - Nucleic Acids Research

JF - Nucleic Acids Research

IS - D1

ER -