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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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植物基因组方面的数据库和网站

2009-11-05 09:28:05| 分类：生信数据库 | 标签： |举报 |字号大中小订阅

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植物基因组方面的数据库和网站

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_r

·   PLEXdb (Plant Expression Database) is a unified public resource for gene expression_r 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_r database and meta-analysis system for studying the expression_r 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_r/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_r 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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