Nucleic Acids Research, 2005, Vol. 33, Database issue D651-D655
© 2005, the authors
Nucleic Acids Research, Vol. 33, Database issue © Oxford University Press 2005; all rights reserved
Rice Annotation Database (RAD): a contig-oriented database for map-based rice genomics
Institute of the Society for Techno-innovation of Agriculture, Forestry and Fisheries, 446-1 Ippaizuka, Kamiyokoba, Tsukuba, Ibaraki 305-0854, Japan, 1 Hitachi Science Systems Co. Ltd, 832-1 Horiguchi, Hitachinaka, Ibaraki 312-0034, Japan, 2 National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan and 3 Mitsubishi Space Software Co. Ltd, 1-6-1 Takezono, Tsukuba, Ibaraki 305-0032, Japan
* To whom correspondence should be addressed. Tel: +81 298 38 2257; Fax: +81 298 38 2302; Email: yuito{at}staff.or.jp
Received June 24, 2004; Revised and Accepted October 12, 2004
A contig-oriented database for annotation of the rice genome has been constructed to facilitate map-based rice genomics. The Rice Annotation Database has the following functional features: (i) extensive effort of manual annotations of P1-derived artificial chromosome/bacterial artificial chromosome clones can be merged at chromosome and contig-level; (ii) concise visualization of the annotation information such as the predicted genes, results of various prediction programs (RiceHMM, Genscan, Genscan+, Fgenesh, GeneMark, etc.), homology to expressed sequence tag, full-length cDNA and protein; (iii) user-friendly clone / gene query system; (iv) download functions for nucleotide, amino acid and coding sequences; (v) analysis of various features of the genome (GC-content, average value, etc.); and (vi) genome-wide homology search (BLAST) of contig- and chromosome-level genome sequence to allow comparative analysis with the genome sequence of other organisms. As of October 2004, the database contains a total of 215 Mb sequence with relevant annotation results including 30 000 manually curated genes. The database can provide the latest information on manual annotation as well as a comprehensive structural analysis of various features of the rice genome. The database can be accessed at http://rad.dna.affrc.go.jp/.
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