Results: 3

1.
Figure 1.

Figure 1. From: eggNOG v3.0: orthologous groups covering 1133 organisms at 41 different taxonomic ranges.

In addition to the over 100 000 orthologous groups in the last universal common ancestor (LUCA), eggNOG v3 also provides orthologous groups and functional annotation for an additional 40 taxonomic levels. Here we display each level with its abbreviated name, species count, orthologous group count and annotation coverage. The annotation coverage for both the functional description of the groups as well as the functional category (in parentheses) is given.

Sean Powell, et al. Nucleic Acids Res. 2012 January;40(Database issue):D284-D289.
2.
Figure 3.

Figure 3. From: eggNOG v3.0: orthologous groups covering 1133 organisms at 41 different taxonomic ranges.

Screenshot of a results page. The eggNOG database was queried for the term ‘smoothened’. The top left picture demonstrates the simplified navigation of multiple search terms and species selection. The navigation tree at the top right of the page allows the user to change the view to more coarse-grained orthologous groups, for example, the mammalian orthologous groups. The group features, such as member proteins, alignments (green arrow) and phylogenetic trees with SMART domains (orange arrow), can be accessed inline and do not require a page refresh.

Sean Powell, et al. Nucleic Acids Res. 2012 January;40(Database issue):D284-D289.
3.
Figure 2.

Figure 2. From: eggNOG v3.0: orthologous groups covering 1133 organisms at 41 different taxonomic ranges.

Quality assessment of eggNOG v3. We used 70 manually curated families (RefOGs) to test the accuracy of orthology prediction of the new release compared to eggNOG v2. For each release, we identified the orthologous group (OG) with the largest overlap of each RefOG and calculated how many genes were not predicted in the OG (missing orthologs) and how many genes were over-predicted in the OG (false assignments). Additionally, we checked if members of the same RefOG have been separated into multiple OGs (RefOG fission) and how many of those OGs include more than three false assignments (RefOG fusion). Missing orthologs influence 41% of the RefOGs; however, this is significantly less than the 57% in eggNOG v2. Similarly, less RefOGs include false assignments in eggNOG v3 (60%) compared to version 2 (66%). However, there are slightly less artificial OG fusions and fissions in eggNOG v2. Given that an addition of species can introduce false assignments, our results suggest that the eggNOG methodology can tolerate a large number of species, and at the same time improve its coverage against the tested benchmark dataset.

Sean Powell, et al. Nucleic Acids Res. 2012 January;40(Database issue):D284-D289.

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