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BioMed Research International
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2014
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Article
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Tab 1
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Research Article
Tools and Databases of the KOMICS Web Portal for Preprocessing, Mining, and Dissemination of Metabolomics Data
Table 1
The tools and databases available at KOMICS (as of November 2013).
Name
Description
URL
Reference
Standalone tools
PowerGet
Metabolite detection, alignment, and annotation tool for LC-high-resolution-MS.
http://www.kazusa.or.jp/komics/software/PowerGet
MatchedIonsFinder
Revising tool for metabolite alignment results from LC-MS analyses.
http://www.kazusa.or.jp/komics/software/MatchedIonsFinder
[
1
]
FragmentAlign
Metabolite alignment and annotation tool for GC-MS.
http://www.kazusa.or.jp/komics/software/FragmentAlign
SpiceHit
High-throughput metabolite detection and annotation tool for SIM analysis in CE-MS.
http://www.kazusa.or.jp/komics/software/SpiceHit
KAGIANA
Microsoft Excel-based tool for exploring the function of
Arabidopsis
genes.
http://webs2.kazusa.or.jp/kagiana/
[
2
]
SokanProject
A tool for calculating Pearson's correlation coefficients.
http://www.kazusa.or.jp/komics/software/SokanProject
Web tools
MFSearcher
Web service for rapid prediction of elemental composition and database searching by accurate mass values.
http://webs2.kazusa.or.jp/mfsearcher/
[
3
]
DAGViz
Visualization tool for similarities of gene ontology annotations.
http://www.pgb.kazusa.or.jp/dagviz/
[
4
]
Databases
MassBase
Largest repository of metabolomics raw data.
http://webs2.kazusa.or.jp/massbase/
KomicMarket
Sample-centric database for metabolomic profile data.
http://webs2.kazusa.or.jp/komicmarket/
New KomicMarket temporary website
Developmental version of KomicMarket.
http://webs2.kazusa.or.jp/new_km_tmp/
KaPPA-View4
Pathway database for visualizing metabolome and transcriptome data.
http://kpv.kazusa.or.jp/
[
5
]
Metabolonote
Metadata-specific Semantic MediaWiki-based database.
http://metabolonote.kazusa.or.jp/
MS-MS Fragment Viewer
Database for MS/MS fragmentation data of 115 flavonoids.
http://webs2.kazusa.or.jp/msmsfragmentviewer/
RnR
Database providing metabolite-to-gene relationships calculated from ~200 transgenic
Arabidopsis
cells.
http://webs2.kazusa.or.jp/kagiana/rnr
CoP
Gene-to-gene coexpression database for 8 plant species calculated using the Confeito algorithm.
http://webs2.kazusa.or.jp/kagiana/cop0911
[
6
]
KATANA
Cross-search system for
Arabidopsis
genes.
http://www.kazusa.or.jp/katana/
[
7
]
ARTRA
Database of probe information of
Arabidopsis
DNA microarray data (developed by Takara Bio Inc.).
http://artra.kazusa.or.jp/artra/ARI3_101/
[
8
]
FuLoja
Database of
Lotus japonicus
full-length cDNA obtained in the NEDO project.
http://webs2.kazusa.or.jp/IntegrationDBRS/FuLoja/
PMPj-Blast
Database of ESTs, cDNAs, and oligo DNA microarray probes for
Lotus japonicus
and some other plants.
http://webs2.kazusa.or.jp/IntegrationDBRS/pmpj-blast/