Similar protocols

Pipeline publication

[…] coverage (see , online). Functional descriptors are based on the most recent eggNOG build, and currently include curated Gene Ontology (GO) terms (), KEGG pathways () and COG functional categories (). Moreover, taking advantage of the fine grained orthology assignments, gene family names are predicted for each query., To test the performance of annotation transfer using orthology relationships, we benchmarked eggNOG-mapper GO predictions for the complete proteomes of five functionally well-characterized model organisms alongside those produced by two existing approaches. The first is standard BLAST homology searches at different E-value thresholds, which is the approach used by tools like Blast2GO () and RAST (). The other is the state-of-the-art InterProScan 5 pipeline (), which unifies twelve independent databases into a manually curated collection of functional models based on sequence profiles. In addition, we evaluated eggNOG-mapper in the context of the second Critical Assessment of protein Function Annotation project (CAFA2), where 126 annotation methods were recently tested (). Finally, using simulated data, we benchmarked eggNOG-mapper for functional annotation of metagenomics samples., As a gold standard for functional assignment, we used experimentally validated GO terms as true positives (TP), and curated taxon exclusion GO data () as false positive terms (FP). GO terms not falling into the true or false positive categori […]

Pipeline specifications

Software tools Blast2GO, RAST, InterProScan