CSRDB: a small RNA integrated database and browser resource for cereals.
CSRDB: a small RNA integrated database and browser resource for cereals.
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CSRDB：用于谷物的小型RNA集成数据库和浏览器资源。
DOI：
10.1093/nar/gkl991
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发表时间：
2007-01
影响因子：
14.9
通讯作者：
Sundaresan, Venkatesan
中科院分区：
文献类型：
--
作者：
Johnson, Cameron;Bowman, Lewis;Adai, Alex T;Vance, Vicki;Sundaresan, Venkatesan
植物小RNA (smRNA)，包括微小RNA (miRNA)、短干扰RNA (siRNA) 和反式作用siRNA (ta-siRNA)，正在成为表观遗传过程以及参与发育和稳态的基因网络的重要组成部分。在这里，我们展示了谷物作物的生物信息学资源，谷物小 RNA 数据库 (CSRDB)，由高通量焦磷酸测序生成的玉米和水稻 smRNA 序列的大规模数据集组成。 smRNA 序列已映射到水稻基因组和可用的玉米基因组序列，这些结果使用通用基因组浏览器呈现在两个基因组浏览器数据集中。 smRNA 的潜在 RNA 靶标已被预测，并且可通过基于 MySQL 的关系数据库访问生成的 smRNA/RNA 靶标对数据集。提供了访问数据的各种方式，包括从基因组浏览器到目标数据库的链接。数据链接和集成是该界面的主要焦点，并且存在内部和外部链接。该资源可在以下位置获取，并将随着更多序列的可用而更新。
Plant small RNAs (smRNAs), which include microRNAs (miRNAs), short interfering RNAs (siRNAs) and trans-acting siRNAs (ta-siRNAs), are emerging as significant components of epigenetic processes and of gene networks involved in development and in homeostasis. Here we present a bioinformatics resource for cereal crops, the Cereal Small RNA Database (CSRDB), consisting of large-scale datasets of maize and rice smRNA sequences generated by high-throughput pyrosequencing. The smRNA sequences have been mapped to the rice genome and to the available maize genome sequence and these results are presented in two genome browser datasets using the Generic Genome Browser. Potential RNA targets for the smRNAs have been predicted and access to the resulting smRNA/RNA target pair dataset has been made available through a MySQL based relational database. Various ways to access the data are provided including links from the genome browser to the target database. Data linking and integration are the main focus for this interface, and internal as well as external links are present. The resource is available at and will be updated as more sequences become available.