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cirad | tropgenedb | oryza tag line | greenphyldb | genoplante home | data | tools | blast | gbrowse the aim of this oryza sativa database was first to display sequence information resulting from the activities of our group, such as the t-dna and ds flanking sequence tags (fsts) produced in the framework of the french genomics initiative genoplante and the eu consortium cereal gene tags. later, we decided to link this information with related molecular data from external rice molecular resources (cdna full length, gene, est, markers, expression data...). genome browser (gbrowse), a web-based application for displaying genomic annotations and other features, is the core of our database. the reference annotation layer consists in the 12 rice pseudomolecules (version 7.0, 0ctober 2011). all the data are superposed as annotations layers and positioned with respect to these pseudomolecules. we developed a set of tools around gbrowse to retrieve as exhaustively as possible information related to queries with several starting points. these tools allow a molecular geneticist to readily find insertion lines (t-dna, tos17, ds) in genes of interest and to retrieve all the associated annotations related to these sequences. breaking news release 7 - unified rice pseudomolecules the 12 rice pseudomolecule sequences are now common to both the msu rice genome annotation project and the rice annotation project database (rap-db)/international rice genome sequencing project . this effort was undertaken in order to allow researchers to easily compare annotations from both the msu and rap-db projects. gene loci, gene models and associated annotations created by msu-rap and rap-db were independently derived, but the pseudomolecules used by the two rice annotation projects to generated those annotations are now identical and can be easily compared. tair10 genome release (november 2010) opening at montpellier, france of the rice functional genomics (refuge) platform : an international hosting platform for elucidating gene function using rice as a model system . [more details] refuge is an international hosting platform for the elucidation of gene function using rice as a model species. it offers international scientists, notably non-rice specialists, an access to know-how, bioinformatic, biological, and molecular resources allowing the use of rice as a model system to investigate gene function through functional genomics strategies. phd and postdoctoral researchers, notably from the south, are the first target beneficiaries of this initiative.visiting scientists have access to the refuge's know-how, including bioinformatic searches, preparation of t-dna vectors, high thoughput production of rice transformants, molecular characterisation of the transformants, genotyping of insertion lines from local and international collections; growth, crossing and phenotyping in containment greenhouse; and access to cell imaging and genotyping platforms. hosted scientists have the opportunity to carry out one to several visits from one to three months, the refuge staff taking care of the materials produced between two visits. the refuge platform provides supervision of the hosted scientists or students and covers bench fees. visitors have to find their own travel and subsistence funds. however, refuge can provide assistance to scientists notably from south countries, to find an appropriate funding source for travel and subsistence. applications should be submitted at http://www.refuge-platform.org and will be readily examined by the refuge scientific committee. funded by agropolis fondation, http://www.agropolis-fondation.fr/ , refuge is a collaborative venture between the joint research unit dap -inra, cirad and montpellier university and agronomy school- and the 'plant genome and development' laboratory at ird and perpignan university. archipelago version 4 - july 2009 is out-it contains 639 new pieces of information for 562 rice genes- 271 pieces of information are new as compared to previous release- this release includes data from kaku et al (pnas 2006) and kimoto-tomiyama et al (pmb 2003) dealing with rice response to chitin elicitor as well as data from zhao et al (tag 2008) dealing with genes responsive to the fngal pathogen rhizoctonia solani. rice annotation release 6.1 (june 2009) we are pleased to inform you that oxford journals has published an update of orygenesdb in nucleic acids research. g. droc ,c. perin, s. fromentin and p. larmande. orygenesdb 2008 update: database interoperability for functional genomics of rice. nucl. acids res advance access published on november 26, 2008. researchers who wish to cite orygenesdb website are encouraged to refer to our publications : g. droc , m. ruiz , p. larmande , a. pereira , p. piffanelli , j. b. morel , a. dievart , b. courtois , e. guiderdoni , and c. perin. orygenesdb: a database for rice reverse genetics. nucl. acids res. 34: d736-d740. centre de cooperation internationale en recherche agronomique pour le developpement cirad 2008 - orygenesdb(at)cirad.fr - last update: november 13, 2012
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