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/