The accuracy of several multiple sequence alignment programs for proteins.
The accuracy of several multiple sequence alignment programs for proteins.
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DOI：
10.1186/1471-2105-7-471
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发表时间：
2006-10-24
影响因子：
3
通讯作者：
Tillier, Elisabeth R M
中科院分区：
文献类型：
--
作者：
Nuin, Paulo A S;Wang, Zhouzhi;Tillier, Elisabeth R M
已经实现了许多算法和软件程序来推断蛋白质和 DNA 序列的多重序列比对。由于对序列进化历史的了解不完整，“真实”比对通常是未知的，因此很难衡量程序的相对准确性。我们测试了九个最常用的蛋白质比对程序，并使用模拟软件 Simprot 生成的序列比较了它们的结果，该软件在现实和受控的进化场景下创建已知的比对。我们使用各种进化历史模拟了 30000 多个比对集，以便定义每个测试程序的优点和缺点。我们发现比对精度极大地依赖于序列中插入和缺失的数量，并且插入缺失大小的影响较弱。我们还考虑了最新版本 BAliBASE 的基准对齐，并且与 BAliBASE 和 Simprot 生成的数据集相关的结果在大多数情况下是一致的。我们的结果表明，与通常的比对精度评估方法相比，使用 Simprot 的模拟序列可以创建更灵活、更广泛的比对类别。 Simprot 还允许对当前可用的比对集中可能不存在的更广泛的可能进化历史进行快速有效的分析。在测试的九个程序中，Mafft (L-INS-i) 和 ProbCons 中提供的迭代方法始终是最准确的，而 Mafft 是两者中速度最快的。
There have been many algorithms and software programs implemented for the inference of multiple sequence alignments of protein and DNA sequences. The "true" alignment is usually unknown due to the incomplete knowledge of the evolutionary history of the sequences, making it difficult to gauge the relative accuracy of the programs. We tested nine of the most often used protein alignment programs and compared their results using sequences generated with the simulation software Simprot which creates known alignments under realistic and controlled evolutionary scenarios. We have simulated more than 30000 alignment sets using various evolutionary histories in order to define strengths and weaknesses of each program tested. We found that alignment accuracy is extremely dependent on the number of insertions and deletions in the sequences, and that indel size has a weaker effect. We also considered benchmark alignments from the latest version of BAliBASE and the results relative to BAliBASE- and Simprot-generated data sets were consistent in most cases. Our results indicate that employing Simprot's simulated sequences allows the creation of a more flexible and broader range of alignment classes than the usual methods for alignment accuracy assessment. Simprot also allows for a quick and efficient analysis of a wider range of possible evolutionary histories that might not be present in currently available alignment sets. Among the nine programs tested, the iterative approach available in Mafft (L-INS-i) and ProbCons were consistently the most accurate, with Mafft being the faster of the two.