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Protocols

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 citations

 (33)
library_books

Clustering of Pan and Core genome of Lactobacillus provides Novel Evolutionary Insights for Differentiation

2018
BMC Genomics
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 […]

library_books

Meta proteomic analysis of protein expression distinctive to electricity generating biofilm communities in air cathode microbial fuel cells

2018
Biotechnol Biofuels
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 […]

library_books

A Large Scale Comparative Metagenomic Study Reveals the Functional Interactions in Six Bloom Forming Microcystis Epibiont Communities

2018
Front Microbiol
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, […]

library_books

Embryophyte stress signaling evolved in the algal progenitors of land plants

2018
Proc Natl Acad Sci U S A
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 […]

library_books

Lignolytic consortium omics analyses reveal novel genomes and pathways involved in lignin modification and valorization

2018
Biotechnol Biofuels
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 […]

library_books

Genome Sequence of a Byssochlamys sp. Strain Isolated from Fouled B20 Biodiesel

2018
Genome Announc
PMCID: 5834322
PMID: 29496830
DOI: 10.1128/genomeA.00085-18

[…] 3.11.1 (), using k-mer values ranging from 21 to 127. genome assembly statistics were computed using quast (). an annotation was then produced using the gensas pipeline (https://www.gensas.org/) and ghostkoala ()., the byssochlamys sp. af001 assembly was composed of 10 scaffolded contiguous sequences. the n50 was 4.6 mbp, the total genome length was 35.9 mbp, and the g+c content was 45.89%. […]


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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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