Arabidopsis Genomics Links
Genome browsers
- GBrowse and SeqViewer at The Arabidopsis Information Resource (TAIR)
http://www.arabidopsis.org/cgi-bin/gbrowse/arabidopsis/
http://www.arabidopsis.org/servlets/sv
- Arabidopsis Ensembl Genome Browser (AtEnsembl)
http://plants.ensembl.org/Arabidopsis_thaliana/Info/Index
- Arabidopsis thaliana Integrated Database (ATIDB)
https://www.ncbi.nlm.nih.gov/pubmed/12582244
- Genoscope Arabidopsis Genome Browser
http://www.genoscope.cns.fr/cgi-bin/ggb/arabidopsis/gbrowse/arabidopsis
- Genome View at MIPS Arabidopsis thaliana Database (MAtDB)
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC308802/
Databases useful for positional cloning
- Monsanto Arabidopsis Polymorphism and Ler Sequence Collections at TAIR
http://www.arabidopsis.org/browse/Cereon/index.jsp
- Multiple SNP Query Tool (MSQT)
http://msqt.weigelworld.org/
- POLYMORPH
http://polymorph.weigelworld.org/
- MarkerTracker at the Bio-Array Resource for Arabidopsis Functional Genomics (BAR)
http://www.bar.utoronto.ca/markertracker/ - The SIGnAL Arabidopsis SNP, Deletion & SFP Database
http://signal.salk.edu/cgi-bin/AtSFP
- Arabidopsis SNP markers from Borevitz Lab
https://borevitzlab.uchicago.edu/resources/molecular-resources ?
- Positional MEDLINE (PosMedSM)
http://omicspace.riken.jp/PosMed/ ?
Databases useful for reverse genetics
- T-DNA Express
http://signal.salk.edu/cgi-bin/tdnaexpress - Seattle Arabidopsis TILLING Project
http://tilling.fhcrc.org/ - Arabidopsis Genomic RNAi Knock-out Line Analysis (AGRIKOLA)
http://www.agrikola.org - Web MicroRNA Designer (WMD)
http://wmd2.weigelworld.org
Global gene expression and co-expression databases
- AtGenExpress
http://www.weigelworld.org/resources/microarray/AtGenExpress/ - NASCArrays
http://affymetrix.arabidopsis.info/narrays/experimentbrowse.pl - BAR
http://bar.utoronto.ca/ - Genevestigator
https://iii.genevestigator.ethz.ch/at/ ? - Arabidopsis Co-expression Data Mining Tools (ACT)
http://www.arabidopsis.leeds.ac.uk/act/index.php - Arabidopsis thaliana Co-expression Network (AraGenNet)
http://aranet.mpimp-golm.mpg.de/aranet - Comprehensive Systems Biology Database (CSB.DB)
http://csbdb.mpimp-golm.mpg.de/ - Platform for RIKEN Metabolomics (PRIMe)
http://prime.psc.riken.jp/ - CressExpress
http://obiwan.ssg.uab.edu:8080/coexpression/index.html - Gene Co-expression Analysis Toolbox (GeneCAT)
http://genecat.mpg.de/cgi-bin/Ainitiator.py - A Complete Arabidopsis Transcriptome MicroArray (CATMA)
http://www.catma.org/
cDNA and EST databases
- Arabidopsis Transcriptome Genomic Analysis Database
http://signal.salk.edu/cgi-bin/atta - T-DNA Express
http://signal.salk.edu/cgi-bin/tdnaexpress - Arabidopsis thaliana Orphan Transcript Database (AtoRNA DB)
http://atornadb.bio.uni-potsdam.de/index.php - Ceres cDNA database
http://www.tigr.org/tdb/e2k1/ath1/ceres/ceres.shtml ? - GenoScope/LifeTechnologies (GSLT) cDNAs
http://www.genoscope.cns.fr/externe/arabidopsis/browser/ - RIKEN Arabidopsis Full-Length (RAFL) cDNA database
http://rarge.gsc.riken.go.jp/cdna/cdna.pl - Salk cDNA and Salk/Stanford/PGEC (SSP) cDNA database -
The Arabidopsis Gene/ORFeome Collection
http://signal.salk.edu/2010/index.html - EST data at TAIR download area
ftp://ftp.Arabidopsis.org/home/tair/Sequences/blast_datasets ?
Small RNA databases
- Arabidopsis Massively Parallel Signature Sequencing (MPSS)
Plus Database
http://mpss.udel.edu/at/ - Arabidopsis thaliana Small RNA Project (ASRP)
http://asrp.cgrb.oregonstate.edu/db/ - miRNA Precursor Candidates for Arabidopsis thaliana
http://sundarlab.ucdavis.edu/mirna/ - Arabidopsis Transcriptome Genomic Analysis Database
http://signal.salk.edu/cgi-bin/atta - Plant snoRNA Database
http://bioinf.scri.sari.ac.uk/cgi-bin/plant_snorna/introduction - Cereal small RNAs Database
http://sundarlab.ucdavis.edu/smrnas/
Protein subcellular localization databases
- SubCellular Proteomic Database (SUBA)
http://www.plantenergy.uwa.edu.au/applications/suba2/ - Plant Proteome DataBase (PPDB)
http://ppdb.tc.cornell.edu/ - Plastid Protein Database (plprot)
http://www.plprot.ethz.ch/ - AtProteome Database
http://fgcz-atproteome.unizh.ch/ - Arabidopsis 2010 Peroxisomal Protein Database
http://www.peroxisome.msu.edu/
Protein-protein interaction databases
- Arabidopsis Interaction Viewer at BAR
http://bar.utoronto.ca/interactions/cgi-bin/arabidopsis_interactions_viewer.cgi - Arabidopsis thaliana Protein Interactome Database (AtPID)
http://atpid.biosino.org/ - Probabilistic Functional Gene Network of Arabidopsis thaliana (AraNet)
http://www.functionalnet.org/aranet/ - Plant Unknown-eome DB (POND)
http://bioinfo.ucr.edu/projects/Unknowns/external/index.html - Arabidopsis Membrane Interactome Project
http://www.associomics.org/
Phenomics
- Phenotypic data in TAIR
- Phenotypic data in NASC
- SENDAI Arabidopsis Seed Stock Center (SASSC)
http://www.shigen.nig.ac.jp/arabidopsis/template.jsp?url=format ? - Bioassay and Phenotype Database (BAP DB)
http://bioweb.ucr.edu/bapdb/ - Riken Arabidopsis Phenome Information Database
http://rarge.gsc.riken.jp/phenome/ - SeedGenes Project Database
http://www.seedgenes.org/ - Chloroplast 2010 Project
http://www.plastid.msu.edu/
Metabolomic databases
- The Golm Metabolome Database (GMD)
http://gmd.mpimp-golm.mpg.de/ - NSF2010 Metabolomics
http://lab.bcb.iastate.edu/projects/plantmetabolomics/ - KNApSAcK
http://kanaya.naist.jp/KNApSAcK/
Database for metabolic and regulatory pathways
- AraCyc at TAIR
http://www.arabidopsis.org/biocyc/index.jsp - Kyoto Encyclopedia of Genes and Genomes (KEGG) Pathway Database
http://www.genome.jp/kegg/pathway.html - The Kazusa Plant Pathway Viewer (KaPPA-View)
http://kpv.kazusa.or.jp/kpv3/guestIndex.jsp - Metabolic Pathway Search at KATANA
http://www.kazusa.or.jp/katana/pathway.html
Spectral databases
- National Institute of Standards and Technology (NIST) Scientific and Technical Databases
http://www.nist.gov/srd/analy.htm - Madison Metabolomics Consortium Database (MMCD)
http://mmcd.nmrfam.wisc.edu/ - MassBank
http://www.massbank.jp/index.html?lang=en - NMRShiftDB
http://nmrshiftdb.ice.mpg.de/ ? - Spectral Database for Organic Compounds (SDBS)
http://riodb01.ibase.aist.go.jp/sdbs/cgi-bin/direct_frame_top.cgi - Biological Magnetic Resonance Data Bank
http://www.bmrb.wisc.edu/metabolomics/ - PRIMe
http://prime.psc.riken.jp/
Seed stock databases
- Arabidopsis Biological Resource Center (ABRC)
http://www.biosci.ohio-state.edu/~plantbio/Facilities/abrc/index.html - European Arabidopsis Stock Centre (NASC)
http://www.arabidopsis.org.uk/ - SALK T-DNA lines
http://signal.salk.edu/ - Lehle Seeds
http://www.arabidopsis.com/ - Arabidopsis thaliana Resource Centre for Genomics
http://www-ijpb.versailles.inra.fr/en/sgap/equipes/variabilite/crg/index.htm - CSHL transposon lines
http://genetrap.cshl.org/ - GABI-Kat T-DNA lines
http://www.gabi-kat.de/ - RIKEN BioResource Center (RIKEN BRC)
http://www.brc.riken.jp/lab/epd/Eng/catalog/seed.shtml