植物基因数据库汇总plant genomics resources
General plant genomics resources
Phytozome: comparative genomics of plants.
PlantGDB: plant genome database
NCBI Plant Genomes Central: Links to NCBI resources for plant genomics.
Munich Information System for Protein Sequences.
Arizona Genome Institute
Clemson University Genomics Institute
ChromatinDB
Carbohydrate active enzymes
Cell Wall Genomics
Primer3 primer design tool
Gene Ontology
Plant Ontology
MicroRNAs
GRIN: Germplasm Resources Information Network
TheVirtual Plant at NYU.
Agricola, a Bibliographic database of citations to the agricultural literature
Phytome supports phylogenetic and functional analyses of predicted protein sequences across plants.
OrthologID provide phylogenetic analysis of Arabidopsis, rice, Populus, and Chlamydomonas genes
PlantTribes provides OrthoMCL clustering of plant proteins, developed as part of the Floral Genome Project.
Gene expression
PLEXdb (Plant Expression Database) is a unified public resource for gene expression for plants and plant pathogens.http://www.plexdb.org
ArrayExpress is a public repository for transcriptomics and related data at EBI.http://www.ebi.ac.uk/arrayexpress/
http://signal.salk.edu
MPSS (Massively Parallel Signature Sequencing) datasets for Arabidopsis, rice, and grape, at U Delaware:http://mpss.udel.edu
Botany Array Resources (BAR).http://www.bar.utoronto.ca
GeneVestigator is a reference expression database and meta-analysis system for studying the expression and regulation of genes by summarizing information from hundreds of microarray experiments into easily interpretable results.https://www.genevestigator.ethz.ch/
Gene Indices and EST resources
The Gene Index project (formerly, TIGR gene indices)http://compbio.dfci.harvard.edu/tgi/
PlantTA: Plant Transcript Assemblieshttp://plantta.tigr.org
HarvEST: EST analysis resources for barley, Brachypodium, Citrus, Coffea, cowpea, soybean, rice, and wheat.http://harvest.ucr.edu/
Arabidopsis resources
TAIR (The Arabidopsis Information Resource) http://www.arabidopsis.org; http://www.tair.org)
Salk Institute Genome Analysis Laboratory.http://signal.salk.edu/
AtGenExpress, a multinational effort to uncover the transcriptome of A. thaliana.http://www.arabidopsis.org/info/expression/ATGenExpress.jsp
Botany Array Resources (BAR).http://www.bar.utoronto.ca
Arabidopsis small RNA projecthttp://asrp.cgrb.oregonstate.edu/
Arabidopsis MPSS data at U Delaware.http://mpss.udel.edu/at/
Grasses and cereals: rice, maize, sorghum, wheat, barley, Brachypodium, et al.
Gramene: A Resource for Comparative Grass Genomicshttp://www.gramene.org
Grain Genes 2.0: A Database for Triticeae and Avena.http://wheat.pw.usda.gov
Sorghum genome sequence at Phytozome:www.phytozome.net/sorghum
MaizeDB (www.maizedb.org)
Maize genome sequence at CSHL (www.maizesequence.org)
Oryza map; maize FPC map. Arizona Genome Institute.http://www.genome.arizona.edu/
Maize and sorghum assembled gene islands (Methyl-filtration)http://magi.plantgenomics.iastate.edu/
Brachpodium genome databasewww.brachybase.org
www.modelcrop.org
Brachypodium genome database at Phytozome:www.phytozome.net/brachypodium
Marker Assisted Selection for wheat.http://maswheat.ucdavis.edu
PanZea: Molecular and Functional Diversity of the Maize Genomewww.panzea.org
Maize Oligonucleotide Array Projecthttp://www.maizearray.org/
Beijing Genome Institute Rice Information System (RISE):http://rise.genomics.org.cn/rice
Rice Annotation Project Database (RAP-DB)http://rapdb.dna.affrc.go.jp/
TIGR rice genome annotation and resources.www.tigr.org/tdb/rice
International Rice Research Institutehttp://www.irri.org/
Rice MPSS data at U. Delawarehttp://mpss.udel.edu/rice/
Legumes: Soybean, Medicago, Lotus, et al.
Soybean genome sequence at Phytozome:www.phytozome.net/soybean
Medicago truncatula: a model for legume research (www.medicago.org). Links to genome sequencing, functional genomics, comparative genomics
Legume Information Systemhttp://www.comparative-legumes.org
Soybase and the soybean breeders toolbox.http://soybase.agron.iastate.edu/
Lotus japonicus genome project at Kazusahttp://www.kazusa.or.jp/lotus/
BeanGenes: a Phaseolus/Vigra database, including links to other useful sites.http://beangenes.cws.ndsu.nodak.edu/
SoyMap: An integrated map of soybean for resolution and dissection of multiple genome duplication events.http://www.soymap.org/
Soybean genome map at Southern Illinois Universityhttp://soybeangenome.siu.edu/
Forest tree genomics
Populus trichocarpa genome at Phytozome.http://www.phytozome.net/poplar
Dendrome is a collection of forest tree genome databases and other forest genetic information resources for the international forest genetics community. Dendrome is part of a larger collaborative effort to construct genome databases for major crop and forest species.http://dendrome.ucdavis.eduEucalyptus
TreeGenes EST database:http://treegenes.ucdavis.edu
PopulusDB expression database at Umea Sweden. http://www.populus.db.umu.se/
Genomic tool development for the chestnut tree and other Fagaceaehttp://www.fagaceae.org/
Other plant species
International Grape Genome Projecthttp://www.vitaceae.org
Grape genome sequence at Genoscope:http://www.genoscope.cns.fr/externe/English/Projets/Projet_ML/index.html
Grape genome at Phytozome:www.phytozome.net/grape
Grape MPSS data at U Delawarehttp://mpss.udel.edu/grape/
Genome Database of Rosaceae (www.bioinfo.wsu.edu/gdr)
Tomato genome project
SOL Genomics Network is a clade-oriented database containing genomic, genetic and taxonomic information for species in the families Solanaceae (e.g., tomato, potato, eggplant, pepper, petunia) and Rubiaceae (coffee). Genomic information is presented in a comparative format and tied to the Arabidopsis genome.www.sgn.cornell.edu
Compositae genomics projecthttp://compgenomics.ucdavis.edu/
Mimulus, columbine
The Physcomitrella patens computational biology resourceshttp://www.cosmoss.org/
Physcomitrella patens genome at Phytozome:www.phytozome.net/physcomitrella
Selaginella moellendorfii genome sequence at Phytozome:www.phytozome.net/selaginella
Castor Bean Genome Database at TIGR.http://castorbean.tigr.org/
Papaya Genome Project at University of Hawaiihttp://cgpbr.hawaii.edu/papaya/
Brassica rapa genome
Cotton genome database contains genomic, genetic and taxonomic information for cotton at USDA-ARS College Station TX.http://cottondb.org/
Cotton Genome Database at the Plant Genome Mapping Laboratory, University of Georgiahttp://www.plantgenome.uga.edu/cotton/StartFrame.htm
International Cotton Genome Initiativehttp://icgi.tamu.edu/
Plant pathogen genomics
Pseudomonas syringae comparative genomicswww.pseudomonas-syringae.org