Morgenstern Burkhard, Prohaska Sonja J, Pöhler Dirk, Stadler Peter F
Universität Göttingen, Institut für Mikrobiologie und Genetik, Abteilung für Bioinformatik, Goldschmidtstrasse, 1, D-37077 Göttingen, Germany.
Algorithms Mol Biol. 2006 Apr 19;1(1):6. doi: 10.1186/1748-7188-1-6.
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.
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.
用于多重比对的自动化软件工具常常无法产生具有生物学意义的结果。在这种情况下，专业知识有助于提高比对的质量。
在此，我们描述了比对程序DIALIGN的半自动版本，它能够考虑预定义的约束条件。用户可以指定序列中假定为同源因而应相互比对的部分。我们的软件程序可以通过创建遵循这些约束条件的多重比对，将这些位点用作锚点。通过这种方式，我们的比对方法能够产生比完全自动化程序产生的比对在生物学上更有意义的比对结果。作为我们方法如何工作的一个示例，我们将我们的方法应用于Hox基因簇周围的基因组序列以及一组DNA结合蛋白。作为一个副产品，我们获得了关于我们的程序用于多重比对的贪婪算法的性能以及潜在目标函数的见解。这些信息将有助于DIALIGN的进一步开发。所描述的比对方法已集成到TRACKER软件系统中。
