DAFS: simultaneous aligning and folding of RNA sequences via dual decomposition
DAFS: simultaneous aligning and folding of RNA sequences via dual decomposition
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DOI：
10.1093/bioinformatics/bts612
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发表时间：
2012-12-01
期刊：
影响因子：
5.8
通讯作者：
Sakakibara, Yasubumi
中科院分区：
文献类型：
--
作者：
Sato, Kengo;Kato, Yuki;Sakakibara, Yasubumi
动机：众所周知，从单个序列预测RNA二级结构的准确性是有限的，因此，如果具有可靠比对的同源序列可用，则从比对序列预测共同二级结构的比较方法是更好的选择。然而，需要正确的二级结构信息来产生RNA序列的可靠比对。为了解决这一困境，我们需要一个快速，准确的比对，考虑到结构信息，以产生可靠的结构比对，这是适合于共同的二级结构prediction.Results：我们开发DAFS，一种新的算法，同时对齐和折叠RNA序列的基础上最大限度地提高预期的准确性预测的共同二级结构及其对齐。DAFS通过对偶分解技术将两两结构比对问题分解为两个独立的二级结构预测问题和一个两两（非结构）比对问题，并通过对不一致的碱基对和比对列施加惩罚来保持两两结构比对的一致性。此外，我们扩展DAFS考虑伪结RNA结构比对集成IPknot预测的伪结结构。在公开数据集上的实验表明，DAFS可以从未比对的序列中产生可靠的结构比对，这与普通二级结构预测的准确性有关。
MOTIVATION: It is well known that the accuracy of RNA secondary structure prediction from a single sequence is limited, and thus a comparative approach that predicts a common secondary structure from aligned sequences is a better choice if homologous sequences with reliable alignments are available. However, correct secondary structure information is needed to produce reliable alignments of RNA sequences. To tackle this dilemma, we require a fast and accurate aligner that takes structural information into consideration to yield reliable structural alignments, which are suitable for common secondary structure prediction.RESULTS: We develop DAFS, a novel algorithm that simultaneously aligns and folds RNA sequences based on maximizing expected accuracy of a predicted common secondary structure and its alignment. DAFS decomposes the pairwise structural alignment problem into two independent secondary structure prediction problems and one pairwise (non-structural) alignment problem by the dual decomposition technique, and maintains the consistency of a pairwise structural alignment by imposing penalties on inconsistent base pairs and alignment columns that are iteratively updated. Furthermore, we extend DAFS to consider pseudoknots in RNA structural alignments by integrating IPknot for predicting a pseudoknotted structure. The experiments on publicly available datasets showed that DAFS can produce reliable structural alignments from unaligned sequences in terms of accuracy of common secondary structure prediction.