Rice Annotation Database (RAD): a contig-oriented database for map-based rice genomics.
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/.
Ito
Yuichi
Y
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
Arikawa
Kohji
K
Antonio
Baltazar A
BA
Ohta
Isamu
I
Naito
Shinji
S
Mukai
Yoshiyuki
Y
Shimano
Atsuko
A
Masukawa
Masatoshi
M
Shibata
Michie
M
Yamamoto
Mayu
M
Ito
Yukiyo
Y
Yokoyama
Junri
J
Sakai
Yasumichi
Y
Sakata
Katsumi
K
Nagamura
Yoshiaki
Y
Namiki
Nobukazu
N
Matsumoto
Takashi
T
Higo
Kenichi
K
Sasaki
Takuji
T
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