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

Abstract

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%).

Depth-stratified functional and taxonomic niche specialization in the ‘core’ and ‘flexible’ Pacific Ocean Virome

“…ORFs that did not map to those data sets were then self-clustered using cd-hit (using the same parameters as above), resulting in a total of 27 685 POV PCs containing X20 ORFs each. These PCs were then annotated using the Similarity Matrix of Proteins (Rattei et al, 2006) to assign taxonomy (NCBI) and function (TIGRFAM), with additional functional information obtained from eggNOG (Powell et al, 2012;4 March 2012).…”

Microbial and viral metagenomes of a subtropical freshwater reservoir subject to climatic disturbances

“…In the group with the highest totaled bit score, the best hit was chosen to annotate the query sequence. To infer Clusters of Orthologous Group (COG), each protein was assigned to the best match in eggNOG (v3.0) database (Powell et al, 2012) using BLASTp with an e-value cutoff of 10 À 5 . Clustered regularly interspaced short palindromic repeats were identified in contigs using PILER-CR (v1.06, http://www.drive5.…”

Uncertain Groupings: Probabilistic Combination of Grouping Data

“…For the evaluation, we constructed a test set of homology data from the Homologene (release 67, [10]), PIRSF (release 2012 03, [15]), and eggNOG (release 3.0, [12]) biological databases. The groupings from each of these databases were loaded into a single database for the construction of trust views and querying.…”

“…Such databases are often made accessible to the scientific community. In our research, we aim to combine the insight into orthologous groupings contained in Homologene [10], PIRSF [15], and eggNOG [12]. An automatic combination of these sources may provide a continuously evolving representation of the current combined scientific insight into orthologous groupings of higher quality than any single heuristic could provide for other bioinformaticians to utilize.…”