Hosoda Masae, Akune Yukie, Aoki-Kinoshita Kiyoko F
Department of Bioinformatics, Graduate School of Engineering, Soka University, Tokyo 192-8577, Japan.
Bioinformatics. 2017 May 1;33(9):1317-1323. doi: 10.1093/bioinformatics/btw827.
A glycan consists of monosaccharides linked by glycosidic bonds, has branches and forms complex molecular structures. Databases have been developed to store large amounts of glycan-binding experiments, including glycan arrays with glycan-binding proteins. However, there are few bioinformatics techniques to analyze large amounts of data for glycans because there are few tools that can handle the complexity of glycan structures. Thus, we have developed the MCAW (Multiple Carbohydrate Alignment with Weights) tool that can align multiple glycan structures, to aid in the understanding of their function as binding recognition molecules.
We have described in detail the first algorithm to perform multiple glycan alignments by modeling glycans as trees. To test our tool, we prepared several data sets, and as a result, we found that the glycan motif could be successfully aligned without any prior knowledge applied to the tool, and the known recognition binding sites of glycans could be aligned at a high rate amongst all our datasets tested. We thus claim that our tool is able to find meaningful glycan recognition and binding patterns using data obtained by glycan-binding experiments. The development and availability of an effective multiple glycan alignment tool opens possibilities for many other glycoinformatics analysis, making this work a big step towards furthering glycomics analysis.
http://www.rings.t.soka.ac.jp.
Supplementary data are available at Bioinformatics online.
聚糖由通过糖苷键连接的单糖组成，具有分支并形成复杂的分子结构。已经开发了数据库来存储大量的聚糖结合实验，包括带有聚糖结合蛋白的聚糖阵列。然而，由于很少有工具能够处理聚糖结构的复杂性，所以几乎没有生物信息学技术来分析大量的聚糖数据。因此，我们开发了MCAW（带权重的多聚糖比对）工具，它可以比对多个聚糖结构，以帮助理解它们作为结合识别分子的功能。
我们详细描述了第一种通过将聚糖建模为树来进行多聚糖比对的算法。为了测试我们的工具，我们准备了几个数据集，结果发现，无需对该工具应用任何先验知识，聚糖基序就能成功比对，并且在我们测试的所有数据集中，聚糖的已知识别结合位点都能以很高的比率比对出来。因此，我们声称我们的工具能够使用通过聚糖结合实验获得的数据找到有意义的聚糖识别和结合模式。一种有效的多聚糖比对工具的开发和可用性为许多其他糖信息学分析开辟了可能性，使这项工作朝着推进糖组学分析迈出了一大步。
http://www.rings.t.soka.ac.jp。
补充数据可在《生物信息学》在线获取。
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