MaxAlign: maximizing usable data in an alignment
MaxAlign: maximizing usable data in an alignment
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DOI：
10.1186/1471-2105-8-312
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发表时间：
2007-08-28
影响因子：
3
通讯作者：
Pedersen, Anders G.
中科院分区：
文献类型：
--
作者：
Gouveia-Oliveira, Rodrigo;Sackett, Peter W.;Pedersen, Anders G.
背景：在核苷酸或蛋白质序列比对中，空位的存在常常给生物信息学研究带来不便。例如，在系统发育分析和其他分析中，有空位的列通常会从比对中完全丢弃。结果：MaxAlign是一个在进行此类分析之前优化比对的程序。具体地说，它通过选择从比对中排除的序列的最佳子集来最大化存在于无空位列（比对区域）中的核苷酸（或氨基酸）符号的数量。MaxAlign可以在系统发育和生物信息学分析之前使用，也可以用于这种形式的比对改进有用的其他情况。在这项工作中，我们测试MaxAlign在这些任务中的性能，并比较系统发育估计的准确性，包括和排除缺口列的分析，有和没有处理与MaxAlign。在本文中，我们还介绍了一种新的简单的树相似性，归一化对称相似性（NSS），我们认为有用的比较树topology.Conclusion：我们演示了如何MaxAlign是有帮助的检测不对齐或有缺陷的序列，而不需要手动检查。我们还表明，这是不可取的，从系统发育分析中排除缺口列，除非MaxAlign首先使用。最后，我们发现MaxAlign从比对中去除的序列往往是那些否则将与低系统发育准确性相关的序列，并且在任何给定序列中存在空位似乎不会干扰其他序列的系统发育估计。cbs. dtu。在dk/ services/ MaxAlign中也可以找到补充信息。2该程序也可以作为Perl独立软件包免费获得。
Background: The presence of gaps in an alignment of nucleotide or protein sequences is often an inconvenience for bioinformatical studies. In phylogenetic and other analyses, for instance, gapped columns are often discarded entirely from the alignment.Results: MaxAlign is a program that optimizes the alignment prior to such analyses. Specifically, it maximizes the number of nucleotide ( or amino acid) symbols that are present in gap- free columns - the alignment area - by selecting the optimal subset of sequences to exclude from the alignment. MaxAlign can be used prior to phylogenetic and bioinformatical analyses as well as in other situations where this form of alignment improvement is useful. In this work we test MaxAlign's performance in these tasks and compare the accuracy of phylogenetic estimates including and excluding gapped columns from the analysis, with and without processing with MaxAlign. In this paper we also introduce a new simple measure of tree similarity, Normalized Symmetric Similarity ( NSS) that we consider useful for comparing tree topologies.Conclusion: We demonstrate how MaxAlign is helpful in detecting misaligned or defective sequences without requiring manual inspection. We also show that it is not advisable to exclude gapped columns from phylogenetic analyses unless MaxAlign is used first. Finally, we find that the sequences removed by MaxAlign from an alignment tend to be those that would otherwise be associated with low phylogenetic accuracy, and that the presence of gaps in any given sequence does not seem to disturb the phylogenetic estimates of other sequences.The MaxAlign web- server is freely available online at http:// www. cbs. dtu. dk/ services/ MaxAlign where supplementary information can also be found. The program is also freely available as a Perl stand- alone package.