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首页> 外文期刊>Dataset Papers in Science >Detection of Introns in Eukaryotic Small Subunit Ribosomal RNA Gene Sequences
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Detection of Introns in Eukaryotic Small Subunit Ribosomal RNA Gene Sequences

机译：真核小亚基核糖体RNA基因序列中内含子的检测

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The gene encoding SSU-rRNA sequences is the tool of choice for phylogenetic analyses and environmental biodiversity analyses of bacteria, Archaea but also unicellular Eukaryota. In Eukaryota, gene sequences may often be interrupted by long or several introns. Searching in GenBank release 188, we found descriptions of 3638 such sequences. Using a database of 180 000 SSU-rRNA sequences well annotated for taxonomy and a C++ program written for that purpose, we computed the presence of 18 691 introns (among which the 3638 described introns). Filtering on length and sequence quality, 3646 sequences were retained. These introns were clustered; clusters were analyzed for the presence of single or multiple clades at various levels of taxonomic depth, allowing future analyses of horizontal transfers. Various analyses of the results are provided as tabulated files as well as FASTA files of described or computed introns. Each sequence is annotated for cellular location (nuclear, chloroplast, and mitochondria), positions at which they were found in the SSU-rRNA sequences and taxonomy as provided by GenBank.
机译：编码SSU-rRNA序列的基因是细菌，古细菌以及单细胞真核生物的系统发育分析和环境生物多样性分析的首选工具。在真核生物中，基因序列可能经常被长或几个内含子打断。在GenBank 188版中进行搜索时，我们找到了3638个此类序列的描述。使用为分类法充分注解的180 000个SSU-rRNA序列数据库和为此目的编写的C ++程序，我们计算出18 691个内含子的存在（其中3638个内含子被描述）。根据长度和序列质量进行筛选，保留了3646个序列。这些内含子是簇状的。对聚类分析了不同分类深度下单个或多个进化枝的存在，以便将来对水平转移进行分析。结果的各种分析以表格文件以及描述或计算的内含子的FASTA文件形式提供。注释每个序列的细胞位置（核，叶绿体和线粒体），在SSU-rRNA序列中发现它们的位置以及GenBank提供的分类法。

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