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http://rgp.dna.affrc.go.jp/giot/INE.html
Sakata,K.2, Mukai,Y.1, Antonio,B.1, Namiki,N.1, Sakai,Y.2, Makino,K.2, Matsumoto,T.1, Sasaki,T.1
1Rice Genome Research Program (RGP), National Institute of Agrobiological Sciences / Institute of the Society for Techno-innovation of Agriculture, Forestry and Fisheries, 446-1 Ippaizuka, Kamiyokoba, Tsukuba, Ibaraki 305-0854, Japan
2Mitsubishi Space Software Co., Ltd., 1-17-15 Sengen, Tsukuba, Ibaraki 305-0047, Japan
Contact tsasaki@nias.affrc.go.jp
The rice genome database INE (INtegrated rice genome Explorer) integrates all the genomic information that has been accumulated from the large scale rice genome analysis including cDNA analysis, genetic mapping, physical mapping as well as the on-going rice genome sequencing project. As part of an effort to accelerate the release of the rice genome sequence to the public domain, 218 Mb of sequence data (as of Sep.5,2002) with 99.99 % accuracy has already been incorporated in the database. The sequence data are integrated with the genetic map, a YAC (yeast artificial chromosome)-based physical map, PAC (P1-derived artificial chromosome) / BAC (bacterial artificial chromosome) contigs and annotation of each clone to facilitate resolution of genomic information at various levels. The recent developments to INE include an EST (Expressed Sequence Tags) map which consists of about 6500 EST markers derived from the large scale cDNA sequencing of rice. A direct correspondence has also been established between the EST map and other available maps. An additional 900 RFLP markers has been incorporated in the genetic map so that the total number of RFLP markers is now 3267. The combined maps provide more markers for map-based cloning and construction of a sequence-ready physical map. The viewing image of the integrated maps has been improved to elucidate the positional relationships among the markers. A relational database scheme by Oracle has been implemented to improve facile access to the database and facilitate a robust searching capability. As for the annotation of the sequences, an automated annotation system called RiceGAAS (Rice Genome Automated Annotation System) has been developed to execute a reliable and up-to-date analysis of the genome sequence as well as to store and retrieve the results of annotation (Sakata et al. 2002).The system collects rice genome sequences from GenBank on a daily basis and executes homology search and gene prediction. All annotated sequence data are stored in the RiceGAAS annotation database and can be retrieved graphically through INE. Thus INE will provide a system for consolidating all the genome sequence data accumulated by the International Rice Genome Sequencing Project (IRGSP) as well as the relevant information in the genome sequence. INE can be accessed at http://rgp.dna.affrc.go.jp/giot/INE.html.
1. Addition of an EST map consisting of 6500markers 2. Addition of 900 RFLP markers in the genetic markers 3. Integration of a relational database scheme by Oracle 4. Integration of the results of automated annotation through RiceGAAS 5. Role of the central database of the IRGSP.
INE was developed by a grant from the Ministry of Agriculture, Forestry and Fisheries of Japan (Rice Genome Project GS-1302).
Sakata et al. 2002. RiceGAAS: an automated annotation system and database for rice genome sequence. Nucleic Acids Research 30,98-102(2002).
Wu,J.et al. A Comprehensive rice transcript map containing 6591 expressed sequence tag sites.Plant Cell 14: 525-535 (2002)
Category Genomic Databases
Go to the abstract in the NAR 2000 Database Issue.