BlastKOALA and GhostKOALA: KEGG Tools for Functional Characterization of Genome and Metagenome Sequences

Abstract

BlastKOALA and GhostKOALA are automatic annotation servers for genome and metagenome sequences, which perform KO (KEGG Orthology) assignments to characterize individual gene functions and reconstruct KEGG pathways, BRITE hierarchies and KEGG modules to infer high-level functions of the organism or the ecosystem. Both servers are made freely available at the KEGG Web site (http://www.kegg.jp/blastkoala/). In BlastKOALA, the KO assignment is performed by a modified version of the internally used KOALA algorithm after the BLAST search against a non-redundant dataset of pangenome sequences at the species, genus or family level, which is generated from the KEGG GENES database by retaining the KO content of each taxonomic category. In GhostKOALA, which utilizes more rapid GHOSTX for database search and is suitable for metagenome annotation, the pangenome dataset is supplemented with Cd-hit clusters including those for viral genes. The result files may be downloaded and manipulated for further KEGG Mapper analysis, such as comparative pathway analysis using multiple BlastKOALA results.

Global occurrence and heterogeneity of the Roseobacter-clade species Ruegeria mobilis

“…Although the core of the four R. mobilis genomes representing the four sub-clusters carry most of the KO orthologs present in the model strains TM1040 and DSS-3 (862 KEGG orthologs, 48%, Figure 3b), they also incorporate a high level of novelty (683 KEGG orthologs, 38%, Figure 3b). In closer comparison, they Figure 3 Genome comparison using (a) the KEGG orthologs of the four Ruegeria mobilis representatives F1926, S1424, NBRC101030 and NBRC102038 (Kanehisa, Sato and Morishima, 2015) and (b) comparing their core KOs (* = 1636 KOs of Figure 3a) to R. pomeroyi DSS-3 and Ruegeria sp. TM1040 using Venny (Oliveros) (details can be found in Supplementary Tables S7 and S8).…”

De novo assembly and characterization of the Hucho taimen transcriptome

“…A KEGG pathway analysis was performed using GhostKOALA (Kanehisa et al., 2016). A total of 51,698 transcripts were assigned to 8,052 KEGG ortholog groups, and among these transcripts, 28,886 were classified into 385 KEGG pathways, including metabolism (6,224 transcripts in 139 pathways), genetic information process (4,966 transcripts in 22 pathways), environmental information process (10,743 transcripts in 38 pathways), cellular processes (8,716 transcripts in 25 pathways), organic systems (11,577 transcripts in 81 pathways), and others (11,543 transcripts in 80 pathways) (Table S5).…”

“…We also used Interproscan to search the protein conserved domains and perform GO classifications (Jones et al., 2014). KEGG annotation was performed using GhostKOALA (Kanehisa, Sato, & Morishima, 2016). …”

Commensal Propionibacterium strain UF1 mitigates intestinal inflammation via Th17 cell regulation

“…The circular map was generated using Blast Ring Image Generator (BRIG) (100). The genome of the P. UF1 was annotated and combined using Rapid Annotation Server (RAST), KEGG Orthology And Links Annotation (KOALA) (101), and Rapid Prokaryotic Genome Annotation (PROKKA) (102). The subsystem categories were summarized and visualized by using RAST.…”