Multiple sequence alignment with user-defined anchor points
Multiple sequence alignment with user-defined anchor points
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DOI：
10.1186/1748-7188-1-6
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发表时间：
2006-01-01
影响因子：
1
通讯作者：
Stadler, Peter F.
中科院分区：
文献类型：
--
作者：
Morgenstern, Burkhard;Prohaska, Sonja J.;Stadler, Peter F.
背景：用于多重比对的自动化软件工具通常不能产生有生物学意义的结果。在这种情况下，专家知识可以帮助提高比对的质量。结果：在这里，我们描述了一个半自动版本的比对程序DIALIGN，可以考虑到预定义的约束。用户可以指定假定为同源的序列部分，因此应相互比对。我们的软件程序可以使用这些网站作为锚点，通过创建一个多重对齐尊重这些约束。这样，我们的比对方法可以产生比全自动程序产生的比对更有生物学意义的比对。作为演示我们的方法是如何工作的，我们将我们的方法应用于Hox基因簇周围的基因组序列和一组DNA结合蛋白。作为一个副产品，我们获得的贪婪算法的性能，我们的程序用于多重比对和有关的目标函数的见解。这些信息将有助于DIALIGN的进一步发展。所描述的对准方法已被集成到TRACKER软件系统中。
Background: Automated software tools for multiple alignment often fail to produce biologically meaningful results. In such situations, expert knowledge can help to improve the quality of alignments.Results: Herein, we describe a semi-automatic version of the alignment program DIALIGN that can take pre-defined constraints into account. It is possible for the user to specify parts of the sequences that are assumed to be homologous and should therefore be aligned to each other. Our software program can use these sites as anchor points by creating a multiple alignment respecting these constraints. This way, our alignment method can produce alignments that are biologically more meaningful than alignments produced by fully automated procedures. As a demonstration of how our method works, we apply our approach to genomic sequences around the Hox gene cluster and to a set of DNA-binding proteins. As a by-product, we obtain insights about the performance of the greedy algorithm that our program uses for multiple alignment and about the underlying objective function. This information will be useful for the further development of DIALIGN. The described alignment approach has been integrated into the TRACKER software system.