JAR3D Webserver: Scoring and aligning RNA loop sequences to known 3D motifs.
JAR3D Webserver: Scoring and aligning RNA loop sequences to known 3D motifs.
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DOI：
10.1093/nar/gkw453
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发表时间：
2016-07-08
影响因子：
14.9
通讯作者：
Leontis N
中科院分区：
文献类型：
--
作者：
Roll J;Zirbel CL;Sweeney B;Petrov AI;Leontis N
许多非编码RNA已被鉴定，并可能通过形成2D和3D结构发挥作用。RNA发夹和内部环在二级结构图上通常表示为非结构化的，但RNA 3D结构表明大多数此类环是由非沃森-克里克碱基对和碱基堆叠结构化的。此外，不同的RNA序列可以形成相同的RNA 3D基序。JAR 3D通过将环序列与RNA 3D Motif Atlas中的基序组匹配，在可能的情况下通过精确序列匹配，以及通过概率评分和编辑距离为新序列找到发夹和内环的可能3D几何形状。评分衡量序列形成在基序的3D结构中观察到的相同相互作用模式的能力。在http://rna.bgsu.edu/jar3d/的JAR 3D网络服务器将单个环的一个或多个序列作为输入，或者将具有多个环的较长RNA的一个或多个序列作为输入。针对所有当前基序组对每个序列进行评分。输出显示了十个最佳匹配的基序组。用户可以将输入序列与JAR 3D发现的每个基序组进行比对。JAR 3D将随着RNA 3D Motif Atlas的每次发布而更新，因此其性能有望随着时间的推移而改善。
Many non-coding RNAs have been identified and may function by forming 2D and 3D structures. RNA hairpin and internal loops are often represented as unstructured on secondary structure diagrams, but RNA 3D structures show that most such loops are structured by non-Watson–Crick basepairs and base stacking. Moreover, different RNA sequences can form the same RNA 3D motif. JAR3D finds possible 3D geometries for hairpin and internal loops by matching loop sequences to motif groups from the RNA 3D Motif Atlas, by exact sequence match when possible, and by probabilistic scoring and edit distance for novel sequences. The scoring gauges the ability of the sequences to form the same pattern of interactions observed in 3D structures of the motif. The JAR3D webserver at http://rna.bgsu.edu/jar3d/ takes one or many sequences of a single loop as input, or else one or many sequences of longer RNAs with multiple loops. Each sequence is scored against all current motif groups. The output shows the ten best-matching motif groups. Users can align input sequences to each of the motif groups found by JAR3D. JAR3D will be updated with every release of the RNA 3D Motif Atlas, and so its performance is expected to improve over time.