A benchmark of multiple sequence alignment programs upon structural RNAs.
A benchmark of multiple sequence alignment programs upon structural RNAs.
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DOI：
10.1093/nar/gki541
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发表时间：
2005
影响因子：
14.9
通讯作者：
Washietl S
中科院分区：
文献类型：
--
作者：
Gardner PP;Wilm A;Washietl S
迄今为止，很少有人尝试根据核酸序列对比对算法进行基准测试。通常，复杂的 PAM 或 BLOSUM 等模型用于比对蛋白质，但不考虑核酸的等效模型；相反，特别的模型通常更受青睐。在这里，我们系统地测试了现有比对算法在结构 RNA 上的性能。这项工作旨在实现以下目标：（i）确定适合将通用序列比对方法应用于结构 RNA 比对问题的条件。这表明研究人员应在何时何地考虑使用辅助信息（例如二级结构）增强比对过程，以及（ii）确定哪些序列比对算法在最广泛的条件下表现良好。我们发现，仅使用当前算法进行序列比对，<50-60% 的序列同一性通常是不合适的。其次，我们注意到，在最广泛的应用范围内，概率方法 ProAlign 和老化的 Clustal 算法通常优于其他基于序列的算法。
To date, few attempts have been made to benchmark the alignment algorithms upon nucleic acid sequences. Frequently, sophisticated PAM or BLOSUM like models are used to align proteins, yet equivalents are not considered for nucleic acids; instead, rather ad hoc models are generally favoured. Here, we systematically test the performance of existing alignment algorithms on structural RNAs. This work was aimed at achieving the following goals: (i) to determine conditions where it is appropriate to apply common sequence alignment methods to the structural RNA alignment problem. This indicates where and when researchers should consider augmenting the alignment process with auxiliary information, such as secondary structure and (ii) to determine which sequence alignment algorithms perform well under the broadest range of conditions. We find that sequence alignment alone, using the current algorithms, is generally inappropriate <50–60% sequence identity. Second, we note that the probabilistic method ProAlign and the aging Clustal algorithms generally outperform other sequence-based algorithms, under the broadest range of applications.
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DOI：
10.1073/pnas.89.22.10915
发表时间：
1992-11-15
影响因子：
11.1
作者：
HENIKOFF, S;HENIKOFF, JG
通讯作者：
HENIKOFF, JG
影响因子：
4.1
作者：
Hudelot, C;Gowri-Shankar, V;Higgs, PG
通讯作者：
Higgs, PG
影响因子：
1.8
作者：
HOFACKER, IL;FONTANA, W;SCHUSTER, P
通讯作者：
SCHUSTER, P
影响因子：
14.9
作者：
Griffiths-Jones, S;Bateman, A;Eddy, SR
通讯作者：
Eddy, SR
影响因子：
3
作者：
Holmes, I
通讯作者：
Holmes, I