GhostKOALA protocols

View GhostKOALA computational protocol

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GhostKOALA specifications

Information


Unique identifier OMICS_20385
Name GhostKOALA
Interface Web user interface
Restrictions to use None
Input data Amino acid sequences.
Input format FASTA
Computer skills Basic
Version 2.0
Stability Stable
Maintained Yes

Maintainer


  • person_outline Kae Morishima <>

Publication for GhostKOALA

GhostKOALA in pipelines

 (5)
2018
PMCID: 5863372
PMID: 29588660
DOI: 10.1186/s13068-018-1073-4

[…] further compared to the pfam [], dbcan [], and eggnog databases [], using the hmmer3 (http://hmmer.janelia.org/) package. a metabolic pathways analysis was performed using the kegg web application ghostkoala []., metagenomic contigs were submitted to binning by coverage and sequence composition using concoct []. assembled contigs were split in chunks of 10 kb prior to read mapping using […]

2017
PMCID: 5773338
PMID: 29375797
DOI: 10.1002/ece3.3735

[…] and gene ontology (go) classifications. we also used interproscan to search the protein conserved domains and perform go classifications (jones et al., ). kegg annotation was performed using ghostkoala (kanehisa, sato, & morishima, )., we first used the conditional reciprocal best blast (crb‐blast) (aubry, kelly, kümpers, smith‐unna, & hibberd, ) algorithm to identify orthologs […]

2017
PMCID: 5773338
PMID: 29375797
DOI: 10.1002/ece3.3735

[…] and plasma membrane (go:0005886) were most abundant and accounted for 29.7%, 28.4%, 19.1%, and 17.1% of the total assigned transcripts, respectively., a kegg pathway analysis was performed using ghostkoala (kanehisa et al., ). 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 […]

2017
PMCID: 5812542
PMID: 28334407
DOI: 10.1093/femsec/fix028

[…] in the bin had an average confidence interval above 90. a genome bin was classified as a mixed bin containing multiple organisms if <80% of the marker genes were assigned to the same phylum. ghostkoala was used to assign proteins a single best-hit kegg ontology number (ko) which was then used to assess kegg metabolic pathways (kanehisa, sato and morishima ). hmmer3 was used for hidden […]

2016
PMCID: 4926282
PMID: 27353502
DOI: 10.1038/srep28810

[…] performed following the strategy developed by campanaro et al.. taxonomy was determined using phylophlan and further refined using phylopythia software. kegg functional analysis was refined using ghostkoala (http://www.kegg.jp/ghostkoala/). reads were aligned on scaffolds larger than 500 bp with bowtie2 software and scaffold coverage was determined with the genome cov software of the bedtools […]


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GhostKOALA in publications

 (32)
PMCID: 5937832
PMID: 29690879
DOI: 10.1186/s12864-018-4601-5

[…] hcluster_matrix with the option –d gower; for selecting the gower distance calculation for clustering []. core- and pan-genome (additional file ) were analyzed with the metagenome analysis tool ghostkoala against “genus_prokaryotes + family_eukaryotes” database using the brite, pathway and module reconstruction algorithm []. brite reconstruction uses kegg brite hierarchies with combined […]

PMCID: 5913794
PMID: 29713380
DOI: 10.1186/s13068-018-1111-2

[…] generation in mfcs, subsequent analysis focused on pois with log2-fold-change > 1 as well as udps in intermediate mfcs (udpis). analysis of kegg pathways enriched among udpis was conducted by ghostkoala, an automated metagenome annotation server that characterizes gene functions and pathways based on kegg orthology sequence assignments []. as for otus, the diversity of genera in early […]

PMCID: 5919953
PMID: 29731741
DOI: 10.3389/fmicb.2018.00746

[…] and annotation of protein-encoding genes were performed by mocat2 (kultima et al., ). the protein-encoding genes of each sample were separately submitted to the automatic annotation server ghostkoala (last updated march 4, 2016) (kanehisa et al., ) to analyze individual gene function and kyoto encyclopedia of genes and genomes (kegg) pathways (kanehisa and goto, ). furthermore, […]

PMCID: 5899452
PMID: 29581286
DOI: 10.1073/pnas.1719230115

[…] including orthology assignment-based reciprocal blastp against a. thaliana tair10 and k. nitens, hmmer-based eggnog-mapper runs () for orthologous group assignment based on eggnog 4.5.1 (), and ghostkoala runs versus kegg (). for localization predictions, we used a perl script to select those transcripts whose orfs included the n-terminal region and predicted the subcellular localization […]

PMCID: 5863372
PMID: 29588660
DOI: 10.1186/s13068-018-1073-4

[…] further compared to the pfam [], dbcan [], and eggnog databases [], using the hmmer3 (http://hmmer.janelia.org/) package. a metabolic pathways analysis was performed using the kegg web application ghostkoala []., metagenomic contigs were submitted to binning by coverage and sequence composition using concoct []. assembled contigs were split in chunks of 10 kb prior to read mapping using […]


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GhostKOALA institution(s)
Institute for Chemical Research, Kyoto University, Uji, Kyoto, Japan; Healthcare Solutions Department, Fujitsu Kyushu Systems Ltd., Hakata-ku, Fukuoka, Japan
GhostKOALA funding source(s)
Partially supported by the National Bioscience Database Center of the Japan Science and Technology Agency.

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