GhostKOALA pipeline

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

 (4)
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 2015). hmmer3 was used […]

2016
PMCID: 4875698
PMID: 27207100
DOI: 10.1186/s12864-016-2684-4

[…] a set of 123,532 previously identified gene models [24] and interproscan annotated a total of 88,951 genes [23]. predicted proteins were assigned to orthologous groups in the kegg database using the ghostkoala mapping tool [25]. a total of 31.6 % of host proteins were assigned, with 72.1 % of these showing similarity to proteins from monocots (additional file 1: table s5)., we observed a drop […]

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

[…] following the strategy developed by campanaro et al.19. taxonomy was determined using phylophlan42 and further refined using phylopythia software43. kegg functional analysis was refined using ghostkoala (http://www.kegg.jp/ghostkoala/). reads were aligned on scaffolds larger than 500 bp with bowtie2 software44 and scaffold coverage was determined with the genome cov software […]

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

[…] by campanaro et al.19. taxonomy was determined using phylophlan42 and further refined using phylopythia software43. kegg functional analysis was refined using ghostkoala (http://www.kegg.jp/ghostkoala/). reads were aligned on scaffolds larger than 500 bp with bowtie2 software44 and scaffold coverage was determined with the genome cov software of the bedtools package45. coverage […]

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.

GhostKOALA reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review GhostKOALA