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Nucleic Acids Research, 2000, Vol. 28, No. 1 97-101
© 2000 Oxford University Press

INE: a rice genome database with an integrated map view

Katsumi Sakata, Baltazar A. Antonio1, Yoshiyuki Mukai1, Hideki Nagasaki1, Yasumichi Sakai2, Kazuyoshi Makino2 and Takuji Sasaki*

Rice Genome Research Program (RGP), National Institute of Agrobiological Resources, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan, 1Institute of the Society for Techno-innovation of Agriculture, Forestry and Fisheries, 446-1 Ippaizuka, Kamiyokoba, Tsukuba, Ibaraki 305-0854, Japan and 2Mitsubishi Space Software Co., Ltd, 1-17-15 Sengen, Tsukuba, Ibaraki 305-0047, Japan

The Rice Genome Research Program (RGP) launched a large-scale rice genome sequencing in 1998 aimed at decoding all genetic information in rice. A new genome database called INE (INtegrated rice genome Explorer) has been developed in order to integrate all the genomic information that has been accumulated so far and to correlate these data with the genome sequence. A web interface based on Java applet provides a rapid viewing capability in the database. The first operational version of the database has been completed which includes a genetic map, a physical map using YAC (Yeast Artificial Chromosome) clones and PAC (P1-derived Artificial Chromosome) contigs. These maps are displayed graphically so that the positional relationships among the mapped markers on each chromosome can be easily resolved. INE incorporates the sequences and annotations of the PAC contig. A site on low quality information ensures that all submitted sequence data comply with the standard for accuracy. As a repository of rice genome sequence, INE will also serve as a common database of all sequence data obtained by collaborating members of the International Rice Genome Sequencing Project (IRGSP). The database can be accessed at http://www. dna.affrc.go.jp:82/giot/INE.html or its mirror site at http://www.staff.or.jp/giot/INE.html

* To whom correspondence should be addressed. Tel: +81 298 38 2199; Fax: +81 298 38 2302; Email: tsasaki@abr.affrc.go.jp


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