Mamit-tRNA, a database of mammalian mitochondrial tRNA primary and secondary structures
Mamit-tRNA, a database of mammalian mitochondrial tRNA primary and secondary structures
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DOI：
10.1261/rna.588407
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发表时间：
2007-08-01
期刊：
影响因子：
4.5
通讯作者：
Florentz, Catherine
中科院分区：
文献类型：
--
作者：
Putz, Joern;Dupuis, Bruno;Florentz, Catherine
Mamit-tRNA（http：mamit-tRNA.u-strasbg.fr）是一个哺乳动物线粒体基因组数据库，已被开发用于破译哺乳动物线粒体tRNA的结构特征，并作为与线粒体tRNA基因点突变相关的人类疾病框架中的有用工具。为了适应快速增长的完整测序哺乳动物线粒体基因组的可用性，Mamit-tRNA已经实现了一个关系数据库，所有注释的tRNA基因都是人工管理和比对的。已集成系统管理工具以提高效率并允许实时更新（来自NCBI的基因库数据库）可用的哺乳动物线粒体基因组。来自150种生物的3000多个tRNA基因序列根据由反密码子三联体定义的氨基酸特异性被分类为22个家族，并根据遗传学组织。每个序列用指示二级结构域的颜色代码线性显示，并且可以转化为可打印的二维（2D）立体式结构。基于系统发生关系或基于结构特性，可以针对给定tRNA特异性内的一级序列的任何组合提取共有和典型2D结构。Mamit-tRNA进一步展示了人类线粒体tRNA基因的静态个体2D结构，以及多态性和病理相关点突变的位置。该网站还提供了一个表格，允许将人类线粒体基因组核苷酸编号轻松转换为传统的tRNA编号。该数据库有望促进线粒体tRNA结构/功能关系的探索，并在病理相关突变分配的框架中帮助临床医生。
Mamit-tRNA (http://mamit-tRNA.u-strasbg.fr), a database for mammalian mitochondrial genomes, has been developed for deciphering structural features of mammalian mitochondrial tRNAs and as a helpful tool in the frame of human diseases linked to point mutations in mitochondrial tRNA genes. To accommodate the rapid growing availability of fully sequenced mammalian mitochondrial genomes, Mamit-tRNA has implemented a relational database, and all annotated tRNA genes have been curated and aligned manually. System administrative tools have been integrated to improve efficiency and to allow real-time update (from GenBank Database at NCBI) of available mammalian mitochondrial genomes. More than 3000 tRNA gene sequences from 150 organisms are classified into 22 families according to the amino acid specificity as defined by the anticodon triplets and organized according to phylogeny. Each sequence is displayed linearly with color codes indicating secondary structural domains and can be converted into a printable two- dimensional (2D) cloverleaf structure. Consensus and typical 2D structures can be extracted for any combination of primary sequences within a given tRNA specificity on the basis of phylogenetic relationships or on the basis of structural peculiarities. Mamit-tRNA further displays static individual 2D structures of human mitochondrial tRNA genes with location of polymorphisms and pathology-related point mutations. The site offers also a table allowing for an easy conversion of human mitochondrial genome nucleotide numbering into conventional tRNA numbering. The database is expected to facilitate exploration of structure/function relationships of mitochondrial tRNAs and to assist clinicians in the frame of pathology- related mutation assignments.