MUSCLE: a multiple sequence alignment method with reduced time and space complexity.
MUSCLE: a multiple sequence alignment method with reduced time and space complexity.
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DOI：
10.1186/1471-2105-5-113
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发表时间：
2004-08-19
影响因子：
3
通讯作者：
Edgar RC
中科院分区：
文献类型：
--
作者：
Edgar RC
在以前的论文中，我们介绍了MUSCLE，一个新的程序，用于创建蛋白质序列的多重比对，给出了算法的简要总结，并显示MUSCLE达到了迄今为止在四个比对精度基准上报告的最高分数。在这里，我们提出了一个更完整的讨论的算法，描述了几个以前未发表的技术，提高生物学的准确性和/或计算的复杂性。我们引入了一个新的选择，MUSCLE-fast，专为高通量应用程序。我们还描述了一个新的协议，用于评估目标函数，对齐两个配置文件。我们比较的速度和准确性的肌肉与CLUSTALW，渐进POA和MAFFT脚本FFTNS 1，最快的以前公布的程序已知的作者。准确性使用四个基准来衡量：BAliBASE，PREFAB，SABmark和SMART。我们测试了三种变体，提供最高的准确性（MUSCLE默认设置），最高的速度（MUSCLE快速），以及两者之间精心选择的妥协（MUSCLE prog）。我们发现MUSCLE-fast是所有测试集上最快的算法，在通常低两到三个数量级的时间内实现了与CLUSTALW相似的平均对齐准确度。MUSCLE-fast能够在21秒内对齐1，000个平均长度为282的序列在当前的台式计算机上。MUSCLE提供了一系列选项，与当前可用的程序相比，这些选项提供了更高的速度和/或对准精度。肌肉是免费提供的。
In a previous paper, we introduced MUSCLE, a new program for creating multiple alignments of protein sequences, giving a brief summary of the algorithm and showing MUSCLE to achieve the highest scores reported to date on four alignment accuracy benchmarks. Here we present a more complete discussion of the algorithm, describing several previously unpublished techniques that improve biological accuracy and / or computational complexity. We introduce a new option, MUSCLE-fast, designed for high-throughput applications. We also describe a new protocol for evaluating objective functions that align two profiles. We compare the speed and accuracy of MUSCLE with CLUSTALW, Progressive POA and the MAFFT script FFTNS1, the fastest previously published program known to the author. Accuracy is measured using four benchmarks: BAliBASE, PREFAB, SABmark and SMART. We test three variants that offer highest accuracy (MUSCLE with default settings), highest speed (MUSCLE-fast), and a carefully chosen compromise between the two (MUSCLE-prog). We find MUSCLE-fast to be the fastest algorithm on all test sets, achieving average alignment accuracy similar to CLUSTALW in times that are typically two to three orders of magnitude less. MUSCLE-fast is able to align 1,000 sequences of average length 282 in 21 seconds on a current desktop computer. MUSCLE offers a range of options that provide improved speed and / or alignment accuracy compared with currently available programs. MUSCLE is freely available at .
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DOI：
10.1093/bioinformatics/8.3.275
发表时间：
1992-06-01
期刊：
COMPUTER APPLICATIONS IN THE BIOSCIENCES
影响因子：
--
作者：
JONES, DT;TAYLOR, WR;THORNTON, JM
通讯作者：
THORNTON, JM
影响因子：
14.9
作者：
Holm, L;Sander, C
通讯作者：
Sander, C
影响因子：
2.1
作者：
Notredame, C
通讯作者：
Notredame, C
影响因子：
10.7
作者：
Müller, T;Spang, R;Vingron, M
通讯作者：
Vingron, M
影响因子：
5.6
作者：
Gotoh, O
通讯作者：
Gotoh, O