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专业背景:计算机科学 研究方向与兴趣: JavaEE-Web软件开发, 生物信息学, 数据挖掘与机器学习, 智能信息系统 目前工作: 基因组, 转录组, NGS高通量数据分析, 生物数据挖掘, 植物系统发育和比较进化基因组学

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转载 植物基因组方面的数据库和网站  

2011-01-26 21:07:16|  分类: 生信数据库 |  标签: |举报 |字号 订阅

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植物基因组方面的数据库和网站(1)


植物基因组方面的数据库和网站 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.
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
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/


植物基因组方面的数据库和网站(2)


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

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