Improved accuracy of multiple ncRNA alignment by incorporating structural information into a MAFFT-based framework.
Improved accuracy of multiple ncRNA alignment by incorporating structural information into a MAFFT-based framework.
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DOI：
10.1186/1471-2105-9-212
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发表时间：
2008-04-25
影响因子：
3
通讯作者：
Toh H
中科院分区：
文献类型：
--
作者：
Katoh K;Toh H
自从功能性非编码 RNA (ncRNA) 的发现以来，RNA 的结构比对变得越来越重要。最近的研究主要基于桑科夫算法的各种近似，在成对结构比对的准确性方面取得了相当大的进步。相反，对于具有两个以上序列的情况，尽管多重结构比对的重要性已被广泛认可，但与传统的基于序列的方法相比，结构比对的实际优点仍不清楚。从准确性和时间复杂度的角度来看，我们采用了不同的方法，从桑科夫算法的直接扩展到多重比对。作为 MAFFT 比对程序的一个新选项，我们开发了一个多 RNA 比对框架 X-INS-i，它通过两个组件合并结构信息的迭代方法构建多重比对：(1) 通过外部成对比对方法（如 SCARNA 或 LaRA）进行成对结构比对，以及 (2) 新的目标函数“四向一致性”，源自每个子比对组在每个时间点的碱基配对概率。 多重对准阶段。 BRAliBASE 基准测试表明，X-INS-i 在配对总和评分 (SPS) 标准方面优于当前可用的其他方法。作为预测常见二级结构的基础，该方法的准确性与目前领先的方法（例如RNA Sampler）相当或更高。 X-INS-i 框架可用于通过任意算法组合构建多重 RNA 比对，以实现成对 RNA 比对和碱基配对概率。源代码可在可用性和要求部分中找到的网页上找到。
Structural alignment of RNAs is becoming important, since the discovery of functional non-coding RNAs (ncRNAs). Recent studies, mainly based on various approximations of the Sankoff algorithm, have resulted in considerable improvement in the accuracy of pairwise structural alignment. In contrast, for the cases with more than two sequences, the practical merit of structural alignment remains unclear as compared to traditional sequence-based methods, although the importance of multiple structural alignment is widely recognized. We took a different approach from a straightforward extension of the Sankoff algorithm to the multiple alignments from the viewpoints of accuracy and time complexity. As a new option of the MAFFT alignment program, we developed a multiple RNA alignment framework, X-INS-i, which builds a multiple alignment with an iterative method incorporating structural information through two components: (1) pairwise structural alignments by an external pairwise alignment method such as SCARNA or LaRA and (2) a new objective function, Four-way Consistency, derived from the base-pairing probability of every sub-aligned group at every multiple alignment stage. The BRAliBASE benchmark showed that X-INS-i outperforms other methods currently available in the sum-of-pairs score (SPS) criterion. As a basis for predicting common secondary structure, the accuracy of the present method is comparable to or rather higher than those of the current leading methods such as RNA Sampler. The X-INS-i framework can be used for building a multiple RNA alignment from any combination of algorithms for pairwise RNA alignment and base-pairing probability. The source code is available at the webpage found in the Availability and requirements section.
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影响因子：
5.8
作者：
Kiryu, Hisanori;Kin, Taishin;Asai, Kiyoshi
通讯作者：
Asai, Kiyoshi
影响因子：
14.9
作者：
Knudsen, B;Hein, J
通讯作者：
Hein, J
影响因子：
2.9
作者：
MCCASKILL, JS
通讯作者：
MCCASKILL, JS
通过修剪动力学编程矩阵，快速成对的结构RNA对齐。
影响因子：
4.3
作者：
Havgaard, Jakob H.;Torarinsson, Elfar;Gorodkin, Jan
通讯作者：
Gorodkin, Jan
DOI：
10.1016/0005-2795(75)90109-9
发表时间：
1975-01-01
期刊：
BIOCHIMICA ET BIOPHYSICA ACTA
影响因子：
--
作者：
MATTHEWS, BW
通讯作者：
MATTHEWS, BW