MitoRes: a resource of nuclear-encoded mitochondrial genes and their products in Metazoa.
MitoRes: a resource of nuclear-encoded mitochondrial genes and their products in Metazoa.
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DOI：
10.1186/1471-2105-7-36
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发表时间：
2006-01-24
影响因子：
3
通讯作者：
D'Elia D
中科院分区：
文献类型：
--
作者：
Catalano D;Licciulli F;Turi A;Grillo G;Saccone C;D'Elia D
线粒体是亚细胞器，在所有真核呼吸细胞的能量产生和其他代谢途径中起着核心作用。在过去的几年里，随着越来越多的基因组被测序，产生了大量的数据，这为将比较分析方法应用于进化和功能基因组学研究提供了前所未有的机会，目的是揭示调控线粒体生物发生和代谢的分子机制。在这种背景下，基因组和蛋白质组数据的代表性数据集的最佳提取问题具有至关重要的意义。核编码的线粒体相关蛋白的专门资源已经存在；然而，目前还没有具有MitoRes相同特征的线粒体数据库，这是MitoNuc数据库的更新，在其结构、数据源和图形界面方面进行了广泛修改。它载有可获得这类数据的任何后生动物物种的核编码线粒体相关产品的数据，还提供了全面的序列数据集(基因、转录本和蛋白质)以及提取和出口的有用工具。MitoRes整合来自公开的外部来源的信息，并自动将其注释到关系数据库中。此外，它还根据蛋白质的序列相似性将蛋白质聚类，并将它们与基因组数据互连。搜索引擎和序列管理工具允许查询/检索数据库内容以及提取和输出准备用于计算机分析的序列(基因、转录本、蛋白质)和相关子序列(内含子、外显子、非编码区、CDS、信号肽和基因侧翼区)。我们在这里描述的工具是为了支持实验室科学家和生物信息学家描述线粒体靶向序列的分子特征和进化而开发的。它提供的检索和提取序列的方式使用户能够克服在综合利用不同生物信息资源时遇到的障碍，并且序列收集的完整性允许在不同生物水平(基因、转录本和蛋白质)进行种内和种间比较。
Mitochondria are sub-cellular organelles that have a central role in energy production and in other metabolic pathways of all eukaryotic respiring cells. In the last few years, with more and more genomes being sequenced, a huge amount of data has been generated providing an unprecedented opportunity to use the comparative analysis approach in studies of evolution and functional genomics with the aim of shedding light on molecular mechanisms regulating mitochondrial biogenesis and metabolism. In this context, the problem of the optimal extraction of representative datasets of genomic and proteomic data assumes a crucial importance. Specialised resources for nuclear-encoded mitochondria-related proteins already exist; however, no mitochondrial database is currently available with the same features of MitoRes, which is an update of the MitoNuc database extensively modified in its structure, data sources and graphical interface. It contains data on nuclear-encoded mitochondria-related products for any metazoan species for which this type of data is available and also provides comprehensive sequence datasets (gene, transcript and protein) as well as useful tools for their extraction and export. MitoRes consolidates information from publicly external sources and automatically annotates them into a relational database. Additionally, it also clusters proteins on the basis of their sequence similarity and interconnects them with genomic data. The search engine and sequence management tools allow the query/retrieval of the database content and the extraction and export of sequences (gene, transcript, protein) and related sub-sequences (intron, exon, UTR, CDS, signal peptide and gene flanking regions) ready to be used for in silico analysis. The tool we describe here has been developed to support lab scientists and bioinformaticians alike in the characterization of molecular features and evolution of mitochondrial targeting sequences. The way it provides for the retrieval and extraction of sequences allows the user to overcome the obstacles encountered in the integrative use of different bioinformatic resources and the completeness of the sequence collection allows intra- and interspecies comparison at different biological levels (gene, transcript and protein).
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影响因子：
14.9
作者：
Hubbard, T;Barker, D;Clamp, M
通讯作者：
Clamp, M
影响因子：
14.9
作者：
Harris, MA;Clark, J;White, R
通讯作者：
White, R
影响因子：
2.1
作者：
Tatusova, TA;Madden, TL
通讯作者：
Madden, TL
影响因子：
14.9
作者：
The UniProt Consortium
通讯作者：
The UniProt Consortium
影响因子：
14.9
作者：
Sardiello, M;Licciulli, F;Caggese, C
通讯作者：
Caggese, C