title: Rice Annotation Database (RAD): a contig-oriented database for map-based rice genomics.
abstract: 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/.
authors.affiliation: Institute of the Society for Techno-innovation of Agriculture, Forestry and Fisheries, 446-1 Ippaizuka, Kamiyokoba, Tsukuba, Ibaraki 305-0854, Japan. yuito@staff.or.jp
authors.forename: Yuichi
authors.initials: Y
authors.lastname: Ito
authors.forename: Kohji
authors.initials: K
authors.lastname: Arikawa
authors.forename: Baltazar A
authors.initials: BA
authors.lastname: Antonio
authors.forename: Isamu
authors.initials: I
authors.lastname: Ohta
authors.forename: Shinji
authors.initials: S
authors.lastname: Naito
authors.forename: Yoshiyuki
authors.initials: Y
authors.lastname: Mukai
authors.forename: Atsuko
authors.initials: A
authors.lastname: Shimano
authors.forename: Masatoshi
authors.initials: M
authors.lastname: Masukawa
authors.forename: Michie
authors.initials: M
authors.lastname: Shibata
authors.forename: Mayu
authors.initials: M
authors.lastname: Yamamoto
authors.forename: Yukiyo
authors.initials: Y
authors.lastname: Ito
authors.forename: Junri
authors.initials: J
authors.lastname: Yokoyama
authors.forename: Yasumichi
authors.initials: Y
authors.lastname: Sakai
authors.forename: Katsumi
authors.initials: K
authors.lastname: Sakata
authors.forename: Yoshiaki
authors.initials: Y
authors.lastname: Nagamura
authors.forename: Nobukazu
authors.initials: N
authors.lastname: Namiki
authors.forename: Takashi
authors.initials: T
authors.lastname: Matsumoto
authors.forename: Kenichi
authors.initials: K
authors.lastname: Higo
authors.forename: Takuji
authors.initials: T
authors.lastname: Sasaki
mesh_terms: D032461:Chromosomes, Plant; D020451:Contig Mapping; D003628:Database Management Systems; D030541:Databases, Genetic; D018745:Genome, Plant; D023281:Genomics; D012275:Oryza / Q000235:genetics*; D014584:User-Computer Interface