RAG: RNA-As-Graphs database - concepts, analysis, and features
RAG: RNA-As-Graphs database - concepts, analysis, and features
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DOI：
10.1093/bioinformatics/bth084
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发表时间：
2004-05-22
期刊：
影响因子：
5.8
通讯作者：
Schlick, T
中科院分区：
文献类型：
--
作者：
Gan, HH;Fera, D;Schlick, T
动机：了解RNA的结构多样性对于识别新的RNA结构和追求RNA基因组学计划至关重要。通过基于保守RNA二级结构和功能特性之间的相关性对RNA二级基序进行分类，我们为预测新的基序提供了一条途径。虽然有几个RNA数据库存在，没有全面的计划是可用于编目的范围和多样性的RNA的结构repertoires.Results：我们的RNA-As-Graphs（RAG）数据库描述和排名所有数学上可能的（包括现有的和候选人）RNA二级图案的基础上的图形枚举技术。我们将RNA二级结构表示为二维图（网络），指定RNA二级结构元件之间的连接，如环，凸起，茎和连接。我们存档RNA树图案的“树图”和其他RNA，包括伪结，一般的“对偶图”。所有的RNA基序都通过图顶点数（序列长度的度量）进行分类，并通过拓扑复杂度进行排名。RAG清单立即提出了新的RNA基序的候选者，无论是天然存在的还是合成的，从而可能刺激新的RNA基序的预测和设计。
Motivation: Understanding RNA's structural diversity is vital for identifying novel RNA structures and pursuing RNA genomics initiatives. By classifying RNA secondary motifs based on correlations between conserved RNA secondary structures and functional properties, we offer an avenue for predicting novel motifs. Although several RNA databases exist, no comprehensive schemes are available for cataloguing the range and diversity of RNA's structural repertoire.Results: Our RNA-As-Graphs (RAG) database describes and ranks all mathematically possible (including existing and candidate) RNA secondary motifs on the basis of graphical enumeration techniques. We represent RNA secondary structures as two-dimensional graphs (networks), specifying the connectivity between RNA secondary structural elements, such as loops, bulges, stems and junctions. We archive RNA tree motifs as 'tree graphs' and other RNAs, including pseudoknots, as general 'dual graphs'. All RNA motifs are catalogued by graph vertex number (a measure of sequence length) and ranked by topological complexity. The RAG inventory immediately suggests candidates for novel RNA motifs, either naturally occurring or synthetic, and thereby might stimulate the prediction and design of novel RNA motifs.