Automated genome annotation and pathway identification using the KEGG Orthology (KO) as a controlled vocabulary

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KOBAS server: a web-based platform for automated annotation and pathway identification (2006, methodology): “We chose BLAST E-value 10 5 and rank 5 as the default cutoffs, meaning that a new sequence is assigned the KO term(s) of the first BLAST hit that (i) has BLAST E-value 10 (5), (ii) has known KO assignments and (iii) has less than five other hits with a lower E-value that do not have KO assignments (”
The OMA orthology database in 2018: retrieving evolutionary relationships among all domains of life through richer web and programmatic interfaces (2017, neutral): “Because orthologs are so important, a large number of methods and resources for their inference have been developed over the years, such as the COGs database (4), Inparanoid (5), OrthoMCL (6), En-sembl Compara (7), KEGG Orthology (8), PhylomeDb (9), OrthoDB (10), EggNOG (11), MBGD (12), PLAZA (13) o”
KOBAS-i: intelligent prioritization and exploratory visualization of biological functions for gene enrichment analysis (2021, methodology): “Taking advantage of the KEGG Orthology Based Annotation System (KOBAS) framework (34) and sequence similarity mapping, the current KOBAS could expand its supported species from 1327 to 5944.”