A simple method to control over-alignment in the MAFFT multiple sequence alignment program.
A simple method to control over-alignment in the MAFFT multiple sequence alignment program.
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DOI：
10.1093/bioinformatics/btw108
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发表时间：
2016-07-01
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影响因子：
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通讯作者：
Standley DM
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文献类型：
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作者：
Katoh K;Standley DM
动机：我们提出了MAFFT多重对齐程序的一个新特性，用于抑制过度对齐（对齐不相关的片段）。传统的MAFFT在比对远程同源物中的保守区域方面高度敏感，但由于测序错误和基因预测困难等原因，蛋白质序列数据库中低质量或有噪声的序列越来越多，因此过度比对的风险最近变得越来越大。结果：该方法基于每对序列的全局相似性，对单个多序列比对中的不同序列对（或组）使用可变评分矩阵。在实际实例和各种条件下的模拟中，该方法显著提高了正确的间隙位置。在灵敏度方面，该方法在基于真实蛋白质的基准测试中效果略负，而在基于模拟的基准测试中效果基本中性。该方法基于自然生物推理，并应兼容许多基于动态规划的多序列比对方法。可用性和实现：新特性在MAFFT 7.263及更高版本中可用。http://mafft.cbrc.jp/alignment/software/联系方式：katoh@ifrec.osaka-u.ac.jp补充信息：补充数据可在Bioinformatics在线获取。
Motivation: We present a new feature of the MAFFT multiple alignment program for suppressing over-alignment (aligning unrelated segments). Conventional MAFFT is highly sensitive in aligning conserved regions in remote homologs, but the risk of over-alignment is recently becoming greater, as low-quality or noisy sequences are increasing in protein sequence databases, due, for example, to sequencing errors and difficulty in gene prediction. Results: The proposed method utilizes a variable scoring matrix for different pairs of sequences (or groups) in a single multiple sequence alignment, based on the global similarity of each pair. This method significantly increases the correctly gapped sites in real examples and in simulations under various conditions. Regarding sensitivity, the effect of the proposed method is slightly negative in real protein-based benchmarks, and mostly neutral in simulation-based benchmarks. This approach is based on natural biological reasoning and should be compatible with many methods based on dynamic programming for multiple sequence alignment. Availability and implementation: The new feature is available in MAFFT versions 7.263 and higher. http://mafft.cbrc.jp/alignment/software/ Contact: katoh@ifrec.osaka-u.ac.jp Supplementary information: Supplementary data are available at Bioinformatics online.