Comprehensive Evaluation of Toxoplasma gondii VEG and Neospora caninum LIV Genomes with Tachyzoite Stage Transcriptome and Proteome Defines Novel Transcript Features
Fig 2
Qualitative and quantitative assessment of manually re-evaluated genomes.
(A) We took confidence scores of Pfam domain hits (Pfam database v 26.0) as a rough indicator of the annotation quality and compared the e-value scores of Pfam domains before and after curation. Repetitive domains were omitted and the copy with the lowest e-value score is used for comparison. A 10-fold change in the e-value was considered as a significant change. While the e-values of Pfam domains in unchanged genes remain the same, we find a general increase in Pfam domain hit significance (decreasing e-values) after our curation (orange). We also find new Pfam domain hits appearing in the corrected genes (green) and in newly created genes (red). (B) Quantitative assessment of manual curation. Functional domain content of a genome is a crude indicator of annotation quality; therefore we compared the proportion of genes having a domain hit from InterProScan (grey) to genes without any domains (black). We find a ~20% increase in genes with functional domains after curation in TgVEG and ~10% in NcLIV genome.