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Rice Annotation Database (RAD): a contig-oriented database for map-based rice genomics.

Yuichi Ito·Kohji Arikawa·Baltazar A Antonio·Isamu Ohta·Shinji Naito·Yoshiyuki Mukai·Atsuko Shimano·Masatoshi Masukawa·Michie Shibata·Mayu Yamamoto·Yukiyo Ito·Junri Yokoyama·Yasumichi Sakai·Katsumi Sakata·Yoshiaki Nagamura·Nobukazu Namiki·Takashi Matsumoto·Kenichi Higo·Takuji Sasaki
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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/.

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Chromosomes, PlantContig MappingDatabase Management SystemsDatabases, GeneticGenome, PlantGenomicsOryzaUser-Computer InterfaceJournal ArticleResearch Support, Non-U.S. Gov't

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Yuichi Ito, Kohji Arikawa, Baltazar A Antonio, Isamu Ohta, Shinji Naito, Yoshiyuki Mukai, Atsuko Shimano, Masatoshi Masukawa, Michie Shibata, Mayu Yamamoto, Yukiyo Ito, Junri Yokoyama, Yasumichi Sakai, Katsumi Sakata, Yoshiaki Nagamura, Nobukazu Namiki, Takashi Matsumoto, Kenichi Higo, Takuji Sasaki. 2005-01-01. Rice Annotation Database (RAD): a contig-oriented database for map-based rice genomics.. https://doi.org/10.1093/nar%2Fgki083

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