Journal: Molecular Biology and Evolution

Article Title: Fast Genome-Wide Functional Annotation through Orthology Assignment by eggNOG-Mapper

doi: 10.1093/molbev/msx148

Figure Lengend Snippet: eggNOG-mapper versus BLAST based Gene Ontology annotations. Comparison of the annotation results for five model species using eggNOG-mapper in HMMER mode (brighter colors) and BLAST (dimmed colors). Left panel shows the per-protein average proportion of true positive GO term assignments (TP, green, experimentally validated) to false positive term assignments (FP, red, derived from taxonomic exclusion criteria). Within each plot, consecutive pairs of horizontal bars represent different BLAST E -value cutoffs ranging from 1E-03 to 1E-40, with sequence matches under this cutoff being excluded from both BLAST and eggNOG-mapper hits. Middle panel shows the per-protein average number of true positive GO term assignments (green), false positive term assignments (red), and assignments of GO terms where neither curated evidence nor taxonomic exclusion criteria holds (grey). Next to the plot is shown the ratio of true positive term assignments (TP-ratio) over the total number of assignments (including false and uncertain terms, CAFA2 approach). Right panel shows the percentage of each proteome that receives annotation, indicating the fraction of proteins that were annotated exclusively with curated true positive terms (TP, blue); proteins annotated with curated terms but also false or uncertain assignments (purple); and proteins that only received false or uncertain assignments (orange, proportion used to compute the no-TP ratio column).

Article Snippet: Predicted eggNOG-mapper annotations were evaluated using the official CAFA2 benchmarking MatLab scripts in partial mode .

Techniques: Comparison, Derivative Assay, Sequencing

Journal: Molecular Biology and Evolution

Article Title: Fast Genome-Wide Functional Annotation through Orthology Assignment by eggNOG-Mapper

doi: 10.1093/molbev/msx148

Figure Lengend Snippet: eggNOG-mapper versus InterProScan. Comparison of the annotation results for five model species using eggNOG-mapper in HMMER mode and with default parameters (brighter colors) and InterProScan (dimmed colors) with default parameters and without further restrictions. The left panel shows the per-protein average proportion of true positive GO term assignments (TP, green, experimentally validated) to false positive term assignments (FP, red, derived from taxonomic exclusion criteria). Consecutive pairs of horizontal bars represent each species in the benchmark. The middle panel shows the per-protein average number of true positive GO term assignments (green), false positive term assignments (red), and assignments of GO terms where neither curated evidence nor taxonomic exclusion criteria hold (grey). Next to the plot is shown the ratio of true positive term assignments (TP-ratio) over the total number of assignments (including false and uncertain assignments, CAFA2 approach). The right panel shows the percentage of each proteome that receives annotation, indicating the fraction of proteins that were annotated exclusively with curated true positive terms (TP, blue); proteins annotated with curated terms but also false or uncertain assignments (purple); and proteins that only received false or uncertain assignments (orange, proportion used to compute the no-TP ratio column).

Article Snippet: Predicted eggNOG-mapper annotations were evaluated using the official CAFA2 benchmarking MatLab scripts in partial mode .

Techniques: Comparison, Derivative Assay

Journal: Molecular Biology and Evolution

Article Title: Fast Genome-Wide Functional Annotation through Orthology Assignment by eggNOG-Mapper

doi: 10.1093/molbev/msx148

Figure Lengend Snippet: eggNOG-mapper under the CAFA2 benchmark. Evaluation of eggNOG-mapper using CAFA2 benchmark data set. Evaluation was carried out on No-Knowledge (NK) benchmark sequences in the partial mode. The coverage of each method is shown within its performance bar. Accuracy of the methods is represented by the F -max measure ( F -max = 1 being a perfect predictor). eggNOG-mapper results (DIAMOND mode) are shown in green. For details on the other methods shown, refer to .

Article Snippet: Predicted eggNOG-mapper annotations were evaluated using the official CAFA2 benchmarking MatLab scripts in partial mode .

Techniques: