Rice Annotation Database (RAD): a contig-oriented database for map-based rice genomics.
Rice Annotation Database (RAD): a contig-oriented database for map-based rice genomics.
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DOI：
10.1093/nar/gki083
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发表时间：
2005-01-01
影响因子：
14.9
通讯作者：
Sasaki T
中科院分区：
文献类型：
--
作者：
Ito Y;Arikawa K;Antonio BA;Ohta I;Naito S;Mukai Y;Shimano A;Masukawa M;Shibata M;Yamamoto M;Ito Y;Yokoyama J;Sakai Y;Sakata K;Nagamura Y;Namiki N;Matsumoto T;Higo K;Sasaki T
为促进基于图谱的水稻基因组学研究，构建了面向基因组序列的水稻基因组数据库。该数据库具有以下功能特点：(1)对p1衍生人工染色体/细菌人工染色体克隆的大量人工注释可以在染色体和基因组水平上合并；（ii）预测基因、各种预测程序（RiceHMM、Genscan、Genscan+、Fgenesh、GeneMark等）结果、与表达序列标签的同源性、全长cDNA和蛋白等注释信息的简洁可视化；（iii）用户友好的克隆/基因查询系统；（iv）核苷酸、氨基酸和编码序列下载功能；(v)基因组的各种特征分析（gc含量、平均值等）；（vi）基因组序列的全基因组同源性搜索（BLAST），以便与其他生物的基因组序列进行比较分析。截至2004年10月，该数据库共包含215 Mb序列和相关注释结果，其中包括30,000个人工整理的基因。该数据库可以提供人工标注的最新信息，以及对水稻基因组各种特征的全面结构分析。该数据库可通过http://rad.dna.affrc.go.jp/访问。
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/.