BlastKOALA protocols

View BlastKOALA computational protocol

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BlastKOALA specifications

Information


Unique identifier OMICS_12302
Name BlastKOALA
Interface Web user interface
Restrictions to use None
Input data An amino acid sequence.
Input format Fasta
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline Kae Morishima <>

Publication for BlastKOALA

BlastKOALA in pipelines

 (9)
2018
PMCID: 5762899
PMID: 29321512
DOI: 10.1038/s41598-017-18630-1

[…] (halomonas hl-48) and gca_000686085.1 (marinobacter hl-58). the genomes were annotated integrating information from the following pipelines: 1) the doe-jgi microbial genome annotation pipeline, blastkoala, and the rast server, as previously described. annotations are available on github (see below) and through img (http://img.jgi.doe.gov). the total number of protein encoding genes […]

2018
PMCID: 5822904
PMID: 29581960
DOI: 10.1155/2018/6897032

[…] and are listed in table . the product length ranged from 150–300 bp., genes were functionally annotated through homologous search of the ncbi nonredundant (nr) protein, kegg [] (http://www.kegg.jp/blastkoala), and pfam [] (http://pfam.xfam.org) databases. subcellular locations of the proteins were predicted using the targetp 1.1 server [] (http://www.cbs.dtu.dk/services/targetp). pathway […]

2018
PMCID: 5935387
PMID: 29727440
DOI: 10.1371/journal.pone.0193831

[…] proteins were categorized by molecular function, biological process and cellular component. kyoto encyclopedia of genes and genomes (kegg) pathway of identified proteins was performed by blastkoala in kegg database (http://www.kegg.jp/). signal peptide was determined by signalp 4.1 server (http://www.cbs.dtu.dk/services/signalp/). subcelluar localization was predicted by targetp 1.1 […]

2017
PMCID: 5379747
PMID: 28374778
DOI: 10.1038/srep45985

[…] search tool (blast) in national center for biotechnology information (ncbi) server using position-specific iterated blast (psi-blast) method, and also selected using protein sequence and name in blastkoala (kegg orthology and links annotation, http://www.kegg.jp/blastkoala), and the uniprot protein database (http:// www.uniprot.org/). multiple alignment was performed by clustal omega. […]

2017
PMCID: 5408105
PMID: 28450507
DOI: 10.1128/genomeA.00224-17

[…] was 39.4%. protein-coding gene (cds) prediction was performed using genemark-es () and resulted in 4,028 cdss and a total of 4,315 exons. gene annotation was obtained combining two strategies: (i) blastkoala () was used to search against a nonredundant set of kegg genes, selecting saccharomycetaceae as the taxonomy group; and (ii) rps blast was used to compare protein sequences with eukaryotic […]


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BlastKOALA in publications

 (77)
PMCID: 5935387
PMID: 29727440
DOI: 10.1371/journal.pone.0193831

[…] proteins were categorized by molecular function, biological process and cellular component. kyoto encyclopedia of genes and genomes (kegg) pathway of identified proteins was performed by blastkoala in kegg database (http://www.kegg.jp/). signal peptide was determined by signalp 4.1 server (http://www.cbs.dtu.dk/services/signalp/). subcelluar localization was predicted by targetp 1.1 […]

PMCID: 5908944
PMID: 29674553
DOI: 10.1128/genomeA.00302-18

[…] descriptions were first annotated based on the homologous genes in other spiroplasma genomes () as identified by orthomcl (). subsequent manual curation was based on the information obtain from the blastkoala tool () and blastp () searches against the ncbi nonredundant database (). putative clustered regularly interspaced short palindromic repeats (crisprs) were identified using crisprfinder […]

PMCID: 5908933
PMID: 29674537
DOI: 10.1128/genomeA.00242-18

[…] guidelines. the p. palleroniana mab3 genome annotation was performed using the ncbi prokaryotic genome annotation pipeline (). functional genome annotation of strain mab3 was performed using blastkoala (). the annotation of genes involved in secondary metabolite production was conducted using antismash ()., the genome of p. palleroniana mab3 contains a single circular chromosome of 6.29 […]

PMCID: 5902951
PMID: 29661228
DOI: 10.1186/s13046-018-0757-8

[…] of mir-760 in humans. the top 50 predicted target genes were analyzed using a freely available web site [] (an automatic annotation server for genome and metagenome sequences http://www.kegg.jp/blastkoala/) to screen for genes related to cellular processes. this analysis revealed batf3 as a potential target of mir-760 (fig. ). to test if batf3 expression is regulated by mir-760, we cloned […]

PMCID: 5898042
PMID: 29686747
DOI: 10.1186/s40793-018-0314-2

[…] using the standard operating procedure of the integrated microbial genomes platform developed by the joint genome institute []. in addition, the genome of m. psychrotolerans hv10-m2 was submitted to blastkoala [] and pathway tools [] to be compared against the kegg [] and metacyc [] databases, respectively, for pathway predictions., the properties of the draft genome of m. psychrotolerans […]


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BlastKOALA institution(s)
Institute for Chemical Research, Kyoto University, Uji, Kyoto, Japan; Healthcare Solutions Department, Fujitsu Kyushu Systems Ltd, Hakata-ku, Fukuoka, Japan; Institute for Chemical Research, Kyoto University, Uji, Kyoto, Japan
BlastKOALA funding source(s)
The KEGG project is partially supported by the National Bioscience Database Center of the Japan Science and Technology Agency. The computational resource for the BlastKOALA and GhostKOALA servers is provided by the Bioinformatics Center, Institute for Chemical Research, Kyoto University.

BlastKOALA review

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Jakub Mrazek

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Web
Great tool to annotate your sequences.. Nice UI, easy to use