植物基因数据库General plant genomics resources

植物基因数据库汇总plant genomics resources

2018-04-26 22:46:50 104
植物基因组数据库,转发过来的,非常实用,以飨读者!


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

  • plant genomics resources