Plant-related online databases

Protein related databases

• PPAP - Plant Proteome Annotation Project
• http://aramemnon.botanik.uni-koeln.de/ - Plant Protein Membrane Database

Nucleotide and related databases

• PLACE - Plant cis-acting regulatory DNA elements db
• PlantCARE - Plant cis-acting regulatory DNA elements db

Gene(s)/protein(s) specific databases/resources

• PLACE - Plant cis-acting regulatory DNA elements db

Miscellaneous

• Plant Gene Register

Species specific databases - Plants

• NAL - AGIS - Access to many plant genome databases at the National Agricultural Library
• Mendel - Plant gene nomenclature database from CPGN
• http://urgv.evry.inra.fr/FLAGdb - FLAGdb++: Integrative database around plant genomes
• http://www.uniprot.org/docs/arath - Arabidopsis UniProtKB/Swiss-Prot entries, gene names and WWW servers
• http://www.arabidopsis.org/ - TAIR: The Arabidopsis Information Resource (arabidopsis.org)
• http://mips.gsf.de/proj/thal/db/ - MATDB: MIPS Arabidopsis thaliana db
• http://wardlab.cbs.umn.edu/arabidopsis/ - AMPL: Arabidopsis Membrane Protein Library
• http://www.p450.kvl.dk - Arabidopsis at PlaCe: Site with info on P450, glucosyltransferases, etc.
• http://www.gramene.org/ - Gramene: A comparative mapping resource for grains
• http://www.uniprot.org/docs/rice Oryza sativa UniProtKB/Swiss-Prot: entries, gene names and WWW servers
• http://rgp.dna.affrc.go.jp/ - Rice Genome Research Program
• http://www.shigen.nig.ac.jp/rice/oryzabase/ - Oryzabase: Japanese rice genome db
• http://rice.plantbiology.msu.edu/ - Rice genome annotation project at MSU (Michigan State University)
• http://beangenes.cws.ndsu.nodak.edu/ - BeanGenes: Beans genome db
• http://brassica.bbsrc.ac.uk/ - Brassica Genome Gateway
• http://www.biology.duke.edu/chlamydb/ - ChlamyDB: Chlamydomonas reinhardtii genome db
• http://www.coffeedna.net/ - CoffeeDNA: Coffee genomics web site
• http://cottondb.org/ - CottonDB: Cotton genome db
• Pisum sativum (pea) web site (in russian)
• TIGR Potato - TIGR Potato Functional Genomics project (at JCVI)
• Snapdragon (A.majus) web site
• DragonDB - Snapdragon Database
• SorghumDB - Sorghum genome db
• DFCI GmGI - DFCI Soybean Gene Index
• SoyBase - Soybean genome db
• http://cgsc.biology.yale.edu/metab.html - SoyBase: Metabolic subset of the soybean genome db
• DFCI LeGI - DFCI Tomato Gene Index
• http://dendrome.ucdavis.edu/ - Forest trees genome db

Maize

• http://www.maizegdb.org/ - MaizeDb: Maize genome database
• http://maize.tigr.org/ - TIGR Maize Database
• http://mtm.cshl.edu/ - Maize targeted mutagenesis databas
• http://www.mrizp.co.yu/emdb/default.htm - The ECP/GR Maize Database
• http://mips.gsf.de/proj/plant/jsf/maize/index.jsp - Maize genome database
• http://sundarlab.ucdavis.edu/smrnas/ - Cereal Small RNA Database: Small RNAs expressed in rice and maize

Rice

• http://www.dna.affrc.go.jp/database/ - Rice Database (RAP-DB)
• http://bioserver.myongji.ac.kr/ricemac.html - The Korea Rice Genome Database
• http://rise.genomics.org.cn/rice/index2.jsp - BGI-RISe - Beijing Genomics Institute Rice Information System Database
• http://rkd.ucdavis.edu/ - Rice Kinase Databse
• http://www.pgcdna.co.jp/wrdb/index.html - Wild Rice Database
• http://red.dna.affrc.go.jp/RED/ - Rice Expression Database
• http://rmd.ncpgr.cn/ - Rice Mutation Database (RMD)
• http://gene64.dna.affrc.go.jp/RPD/main_en.html - Rice Proteome Database (RPD)
• http://www.iris.irri.org:8080/IRFGC/ir64.shtml - IR64 Rice Mutant Database
• http://www.gramene.org/resources/ - Complete Rice (Oryza sp.) Sequences
• http://mpss.udel.edu/rice/ - Rice MPSS Database
• http://btn.genomics.org.cn:8080/rice/ - Rice GD (Genome database of Chinese super hybrid rice)
• http://ricetfdb.bio.uni-potsdam.de/v2.0/ - Rice transcription factor database
• http://ricegaas.dna.affrc.go.jp/rgadb/ - RiceGAAS: Rice Genome Annotation Database
• http://mips.gsf.de/proj/plant/jsf/rice/index.jsp - The MIPS Oryza sativa Database (MOsDB)
• http://sundarlab.ucdavis.edu/smrnas/ - Cereal Small RNA Database: Small RNAs expressed in rice and maize

Other

• http://ukcrop.net/ - The UK Crop Plant Bioinformatics Network
• http://www.plantgdb.org/ - PlantGDB: Plant Genome Research Through PlantGDB
• http://www.plantgdb.org/AtGDB/ - PlantGDB - AtGDB: Arabidopsis thaliana Genome
• http://www.plantgdb.org/ASIP/ - PlantGDB - ASIP: Alternative Splicing in Plants
• http://www.agbase.msstate.edu/ - AgBase: GO annotations for agriculturally important plants and animals
• http://urgv.evry.inra.fr/CATdb - CATdb: Arabidopsis transcriptome data
• http://www.tigr.org/tdb/e2k1/ath1/ath1.shtml - The TIGR Arabidopsis thaliana Genome Annotation Database
• http://plantsp.sdsc.edu/ - PlantP: Functional Genomics of Plant Phosphorylation
• http://lipids.plantbiology.msu.edu/ - The Arabidopsis Lipid Gene Database
• Homologous http://chibba.agtec.uga.edu/duplication/ - Plant Genome Duplication Database
• Inhibitor http://www.ba.itb.cnr.it/PLANT-PIs/ - PLANT-PIs: A database for protease inhibitors and their genes in higher plants
• Insertion http://sundarlab.ucdavis.edu/ - Functional Genomics of Model Plants
• http://podb.nibb.ac.jp/Organellome/ - The Plant Organelles Database is a specialized database project dedicated for plant organelle research.
• Oligo http://www.maizearray.org/maize_search_basic.shtml - Maize Oligonucleotide Array Project
• Oligo http://www.ricearray.org/rice_search_basic.shtmlGenes - Rice Oligonucleotide Array Project
• Pest http://www.planthealthaustralia.com.au/appd/index.asp - Australian Plant Pest Database
• Pest http://infoagro.net/health/caraphin/plantpest.cfm - PLANT PEST DATABASE
• http://mips.gsf.de/projects/plants - MIPSPlantsDB - MIPS Plants Databases. The MIPS plant genomics group focuses on the bioinformatics of plant genomes.
• http://plantsubq.genomics.purdue.edu/ - PlantsUBQ - A Functional Genomics Database for the Ubiquitin/26S Proteasome Proteolytic Pathway in Plants
• http://aramemnon.botanik.uni-koeln.de/ - Plant Protein Membrane Database
• http://w3lamc.umbr.cas.cz/PlantSat/ - PlantSat (A Database Of Plant Satellite Dna)
• http://www.drastic.org.uk/ - DRASTIC: Database resource for analysis of signal transduction in plant cells
• Species http://www.fs.fed.us/database/feis/plants/index.html - Plant Species Life Form
• Taxonomy http://www.ars-grin.gov/cgi-bin/npgs/html/index.pl - GRIN Taxonomy for Plants
• Virus http://www.ncbi.nlm.nih.gov/ICTVdb/ - Virus databases online
• Virus http://image.fs.uidaho.edu/vide/ - Plant Viruses Online

Plant Bioinformatics

• http://www.ebi.ac.uk/embl/ - EMBL Nucleotide Sequence Database
• http://www.ebi.ac.uk/GenomeReviews/ - EMBL Nucleotide Sequence Database - Genome Reviews
• http://www.ncbi.nlm.nih.gov/genbank/ - GenBank
• http://www.ncbi.nlm.nih.gov/ - A Collection of Plant-Specific Genomic Data and Resources at the National Center for Biotechnology Information
• http://www.uniprot.org/ - UniProt
• http://www.uniprot.org/help/uniprotkb - The UniProt Knowledgebase (UniProtKB)
• http://www.expasy.org/ - ExPASy: SIB Bioinformatics Resource Portal
• http://www.jcvi.org/ - Plant Database Resources at The Institute for Genomic Research (TIGR) - now part of J. Craig Venter Institute
• http://mips.helmholtz-muenchen.de/plant/genomes.jsp - Plant Database Resources at The Institute for Genomic Research
• http://harvest.ucr.edu/ - HarvEST originated as EST database-viewing software in support of gene function analyses and oligonucleotide design, then grew to support activities including microarray content design, SNP identification, genotyping platform design, comparative genomics and the coupling of physical and genetic maps.
• http://www.harvest-web.org/ - HarvEST:Web
• http://www.arabidopsis.org/ - The Arabidopsis Information Resource (TAIR) database
• http://atensembl.arabidopsis.info/index.html - AtEnsembl - A post-genomic resource browser for Arabidopsis
• http://www.comparative-legumes.org/ - Legume Information System (LIS)
• http://medicago.org/ - Medicago truncatula
• http://rice.genomics.org.cn/rice/index2.jsp - BGI-RIS V2: Rice Information System at the Beijing Genomics Institute
• http://wheat.pw.usda.gov/GG2/index.shtml - GrainGenes 2.0: A Genomic Database for Triticeae and Avena
• http://www.gramene.org/ - Gramene: A Resource for Comparative Grass Genomics
• http://www.maizegdb.org/ - MaizeGDB: The Maize Genetics and Genomics Database
• http://www.plexdb.org/plex.php?database=Barley - BarleyBase: MIAME/Plant-compliant and Plant Ontology enhanced expression resources for Barley (http://www.barleybase.org/)
• http://plexdb.org/ - Plant Expression Database. Plant Ontology enhanced expression database
• BeanGenes - KEGG: Kyoto Encyclopedia of Genes and Genomes

Gene Ontology Annotation (GO)

• http://www.geneontology.org/ - Gene Ontology Consortium
• http://www.gramene.org/plant_ontology/ - Gramene: Plant Ontology (PO)
• http://www.ebi.ac.uk/QuickGO/ - EBI QuickGO GO browser
• http://www.ihop-net.org/UniPub/iHOP/ - iHOP - Information Hyperlinked over Proteins
• http://www.ebi.ac.uk/Tools/pfa/iprscan/ - InterProScan Sequence Search