Plant Genome Databases and Websites General plant genomics resources Phytozome : comparative genomics of plants. PlantGDB : plant genome database NCBI Plant Genomes Central : Links to NCBI resources for plant genomics. M unich I nformation System for P rotein S equences. 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 The Virtual 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 Assemblies http://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 project http://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 Genomics http://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 database www.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 Genome www.panzea.org Maize Oligonucleotide Array Project http://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 Institute http://www.irri.org/ Rice MPSS data at U. Delaware http://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 System http://www.comparative-legumes.org Soybase and the soybean breeders toolbox. http://soybase.agron.iastate.edu/ Lotus japonicus genome project at Kazusa http://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 University http://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.edu Eucalyptus 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 Fagaceae http://www.fagaceae.org/ Other plant species International Grape Genome Project http://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 Delaware http://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 project http://compgenomics.ucdavis.edu/ Mimulus, columbine The Physcomitrella patens computational biology resources http://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 Hawaii http://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 Georgia http://www.plantgenome.uga.edu/cotton/StartFrame.htm International Cotton Genome Initiative http://icgi.tamu.edu/ Plant pathogen genomics Pseudomonas syringae comparative genomics www.pseudomonas-syringae.org 转自： 紫斑风铃的BLOG http://blog.sina.com.cn/heguo
标签: 植物基因组
