TriFLDB: A Database of Clustered Full-Length Coding Sequences from Triticeae with Applications to Comparative Grass Genomics
TriFLDB: A Database of Clustered Full-Length Coding Sequences from Triticeae with Applications to Comparative Grass Genomics
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DOI：
10.1104/pp.109.138214
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发表时间：
2009-07-01
期刊：
影响因子：
7.4
通讯作者：
Shinozaki, Kazuo
中科院分区：
文献类型：
--
作者：
Mochida, Keiichi;Yoshida, Takuhiro;Shinozaki, Kazuo
小麦族全长CDS数据库（TriFLDB）包含关于小麦族作物小麦（Triticum aestivum）和大麦（Hordeum vulgare）的全长编码序列（CDS）的可用信息，并包括功能注释和比较基因组学特征。TriFLDB提供了一个搜索界面，使用关键字的基因功能和相关的基因本体论术语和DNA的相似性搜索和推导翻译的氨基酸序列，以访问小麦族全长CDS（TriFLCDS）条目的注释。注释由几个序列数据库的相似性搜索结果和InterProScan的结构域预测组成。TriFLDB中推导的氨基酸序列与拟南芥（Arabidopsis thaliana）、水稻（Oryza sativa）和高粱（Sorghum bicolor）的蛋白质组数据集在序列同一性的逐步阈值中通过层次聚类进行分组，提供基于全长蛋白质序列的层次聚类结果。该数据库还提供了基于TriFLCDS到水稻和高粱基因组序列的比较映射的序列相似性结果，其与当前注释一起可用于预测TriFLCDS条目的基因结构。为了提供全长CDS的可能的遗传位置，TriFLCDS条目也被分配到大麦和二倍体小麦的遗传映射的cDNA序列，这是目前容纳在小麦族映射EST数据库。这些关系数据可以从两个数据库的搜索界面中搜索到。目前的TriFLDB包含来自大麦和小麦的15，871个全长CDS，并包括大麦和小麦的推定全长cDNA，这些cDNA可公开获得。这些内容为小麦族基因组学和禾本科比较基因组学提供了一个信息学门户。TriFLDB可在http://TriFLDB.psc.riken.jp/上公开获取。
The Triticeae Full-Length CDS Database (TriFLDB) contains available information regarding full-length coding sequences (CDSs) of the Triticeae crops wheat (Triticum aestivum) and barley (Hordeum vulgare) and includes functional annotations and comparative genomics features. TriFLDB provides a search interface using keywords for gene function and related Gene Ontology terms and a similarity search for DNA and deduced translated amino acid sequences to access annotations of Triticeae full-length CDS (TriFLCDS) entries. Annotations consist of similarity search results against several sequence databases and domain structure predictions by InterProScan. The deduced amino acid sequences in TriFLDB are grouped with the proteome datasets for Arabidopsis (Arabidopsis thaliana), rice (Oryza sativa), and sorghum (Sorghum bicolor) by hierarchical clustering in stepwise thresholds of sequence identity, providing hierarchical clustering results based on full-length protein sequences. The database also provides sequence similarity results based on comparative mapping of TriFLCDSs onto the rice and sorghum genome sequences, which together with current annotations can be used to predict gene structures for TriFLCDS entries. To provide the possible genetic locations of full-length CDSs, TriFLCDS entries are also assigned to the genetically mapped cDNA sequences of barley and diploid wheat, which are currently accommodated in the Triticeae Mapped EST Database. These relational data are searchable from the search interfaces of both databases. The current TriFLDB contains 15,871 full-length CDSs from barley and wheat and includes putative full-length cDNAs for barley and wheat, which are publicly accessible. This informative content provides an informatics gateway for Triticeae genomics and grass comparative genomics. TriFLDB is publicly available at http://TriFLDB.psc.riken.jp/.