GISSD: Group I Intron Sequence and Structure Database.
GISSD: Group I Intron Sequence and Structure Database.
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DOI：
10.1093/nar/gkm766
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发表时间：
2008-01
影响因子：
14.9
通讯作者：
Zhang Y
中科院分区：
文献类型：
--
作者：
Zhou Y;Lu C;Wu QJ;Wang Y;Sun ZT;Deng JC;Zhang Y
GISSD （Group I内含子序列和结构数据库）是一个专门的、全面的I内含子数据库，专注于从现有数据库中整合有用的I内含子信息，并提供从头开始的数据，这对于在系统水平上理解这些内含子至关重要。该数据库包含1789个完整的内含子记录，包括每个带注释的内含子的核苷酸序列，加上上游和下游外显子的15nt，以及通过整合比较序列分析和最小自由能算法预测的含有假结的二级结构。这些内含子代表了所有14个亚群，并分别提供了它们基于结构的排列。结构预测和对齐都是手动完成的，并迭代调整，这为每个子组产生了可靠的共识结构。这些共识结构使我们能够对INFERNAL程序先前发现的2085个I族内含子的置信度进行判断，并自动将它们分类为子群。该数据库提供了来自GenBank的内含子相关分类信息，允许人们查看所有I类内含子的详细分布。内含子中的cds和三维结构信息也被整合。大约17000个I族内含子已在该数据库中得到验证；其中95%属于IC3亚群，位于叶绿体tRNALeu基因中。GISSD数据库可通过http://www.rna.whu.edu.cn/gissd/访问
Group I Intron Sequence and Structure Database (GISSD) is a specialized and comprehensive database for group I introns, focusing on the integration of useful group I intron information from available databases and providing de novo data that is essential for understanding these introns at a systematic level. This database presents 1789 complete intron records, including the nucleotide sequence of each annotated intron plus 15 nt of the upstream and downstream exons, and the pseudoknots-containing secondary structures predicted by integrating comparative sequence analyses and minimal free energy algorithms. These introns represent all 14 subgroups, with their structure-based alignments being separately provided. Both structure predictions and alignments were done manually and iteratively adjusted, which yielded a reliable consensus structure for each subgroup. These consensus structures allowed us to judge the confidence of 20 085 group I introns previously found by the INFERNAL program and to classify them into subgroups automatically. The database provides intron-associated taxonomy information from GenBank, allowing one to view the detailed distribution of all group I introns. CDSs residing in introns and 3D structure information are also integrated if available. About 17 000 group I introns have been validated in this database; ∼95% of them belong to the IC3 subgroup and reside in the chloroplast tRNALeu gene. The GISSD database can be accessed at http://www.rna.whu.edu.cn/gissd/
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DOI：
10.1073/pnas.0337743100
发表时间：
2003-02-18
影响因子：
11.1
作者：
Rangan, P;Masquida, B;Woodson, SA
通讯作者：
Woodson, SA
影响因子：
56.9
作者：
KUHSEL, MG;STRICKLAND, R;PALMER, JD
通讯作者：
PALMER, JD
影响因子：
14.9
作者：
Li Z;Zhang Y
通讯作者：
Zhang Y
影响因子：
5.6
作者：
MICHEL, F;WESTHOF, E
通讯作者：
WESTHOF, E
影响因子：
14.9
作者：
Griffiths-Jones S;Moxon S;Marshall M;Khanna A;Eddy SR;Bateman A
通讯作者：
Bateman A