Comparative plant genomics resources at PlantGDB
Comparative plant genomics resources at PlantGDB
复制标题
DOI：
10.1104/pp.104.059212
复制
发表时间：
2005-10-01
期刊：
影响因子：
7.4
通讯作者：
Brendel, V
中科院分区：
文献类型：
--
作者：
Dong, QF;Lawrence, CJ;Brendel, V
PlantGDB（http：//www.plantgdb.org/）是植物分子序列的数据库。表达序列标签（EST）序列被组装成代表试探性独特基因的重叠群。EST重叠群用来源于与推定的翻译产物高度相似的已知蛋白质序列的信息进行功能注释。暂定基因本体论术语被分配以匹配所鉴定的相似序列的那些。类似地组装基因组调查序列。将得到的基因组调查序列重叠群与EST和保守蛋白质同源物匹配，以鉴定推定的全长开放阅读框架包含基因，随后根据已建立的基因家族命名对其进行临时分类。对于拟南芥（Arabidopsis thaliana）和水稻（Oryza sativa），基因结构的外显子-内含子边界通过EST和全长cDNA与其各自的完整基因组序列的剪接比对来注释。已经开发了独特的基因组浏览器来呈现当前转录物模型的所有可用EST和cDNA证据（对于拟南芥，参见AtGDB网站http://www.plantgdb.org/ AtGDB/;对于水稻，参见OsGDB网站http：//www.plantgdb.org/OsGDB/）。此外，PlantGDB还集成了许多生物信息学工具，使研究人员能够使用自己的数据和数据库中的数据进行现场序列分析。
PlantGDB (http://www.plantgdb.org/)is a database of plant molecular sequences. Expressed sequence tag (EST) sequences are assembled into contigs that represent tentative unique genes. EST contigs are functionally annotated with information derived from known protein sequences that are highly similar to the putative translation products. Tentative Gene Ontology terms are assigned to match those of the similar sequences identified. Genome survey sequences are assembled similarly. The resulting genome survey sequence contigs are matched to ESTs and conserved protein homologs to identify putative full-length open reading frame-containing genes, which are subsequently provisionally classified according to established gene family designations. For Arabidopsis (Arabidopsis thaliana) and rice (Oryza sativa), the exon-intron boundaries for gene structures are annotated by spliced alignment of ESTs and full-length cDNAs to their respective complete genome sequences. Unique genome browsers have been developed to present all available EST and cDNA evidence for current transcript models (for Arabidopsis, see the AtGDB site at http://www.plantgdb.org/AtGDB/; for rice, see the OsGDB site at http://www.plantgdb.org/ OsGDB/). In addition, a number of bioinformatic tools have been integrated at PlantGDB that enable researchers to carry out sequence analyses on-site using both their own data and data residing within the database.