The GlycanBuilder: a fast, intuitive and flexible software tool for building and displaying glycan structures.
The GlycanBuilder: a fast, intuitive and flexible software tool for building and displaying glycan structures.
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DOI：
10.1186/1751-0473-2-3
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发表时间：
2007-08-07
影响因子：
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通讯作者：
Haslam SM
中科院分区：
文献类型：
--
作者：
Ceroni A;Dell A;Haslam SM
碳水化合物在人类疾病中起着关键作用，其作为病理条件的生物标志物的潜在效用是表征糖组的主要驱动力。然而，与蛋白质和核酸相比，聚糖的额外复杂性已经减缓了与基因组学和蛋白质组学相比的糖组学的进展。碳水化合物的分支性质，其成分的巨大多样性和众多的替代符号，使得聚糖的输入和显示不像蛋白质的氨基酸序列那样简单。提供用户界面的每个糖信息学工具将受益于用于以计算机可读格式输入和输出聚糖结构的快速、直观、吸引人的机制。这里描述了一种使用选定的符号表示法构建和显示聚糖结构的软件工具。“GlycanBuilder”使用自动绘制算法绘制糖符号并将其放置在绘图板上。有关符号表示法的信息来自可配置的图形模型，作为一组规则，管理残基和键的方面和位置。该算法能够表示一个结构，只使用很少的遍历树，是固有的快速。该工具使用XML格式导入和导出编码结构。这里描述的渲染算法能够以选定的符号表示法产生聚糖结构的高质量表示。自动绘制过程使“GlycanBuilder”既可用作显示聚糖的用户独立组件，也可用作易于使用的绘图工具。“GlycanBuilder”可以作为Java小程序集成到网页中，用于聚糖的可视化编辑。相同的组件可以作为Web服务来将编码的结构呈现为图形格式。最后，“GlycanBuilder”可以集成到其他应用程序中，以创建直观和吸引人的用户界面：一个例子是“Glycobiridium”，一个用于聚糖质谱辅助注释的软件工具。“GlycanBuilder”代表了一个灵活、可靠和有效的解决方案，可以解决任何糖组学工具或数据库中聚糖结构的输入和输出问题。
Carbohydrates play a critical role in human diseases and their potential utility as biomarkers for pathological conditions is a major driver for characterization of the glycome. However, the additional complexity of glycans compared to proteins and nucleic acids has slowed the advancement of glycomics in comparison to genomics and proteomics. The branched nature of carbohydrates, the great diversity of their constituents and the numerous alternative symbolic notations, make the input and display of glycans not as straightforward as for example the amino-acid sequence of a protein. Every glycoinformatic tool providing a user interface would benefit from a fast, intuitive, appealing mechanism for input and output of glycan structures in a computer readable format. A software tool for building and displaying glycan structures using a chosen symbolic notation is described here. The "GlycanBuilder" uses an automatic rendering algorithm to draw the saccharide symbols and to place them on the drawing board. The information about the symbolic notation is derived from a configurable graphical model as a set of rules governing the aspect and placement of residues and linkages. The algorithm is able to represent a structure using only few traversals of the tree and is inherently fast. The tool uses an XML format for import and export of encoded structures. The rendering algorithm described here is able to produce high-quality representations of glycan structures in a chosen symbolic notation. The automated rendering process enables the "GlycanBuilder" to be used both as a user-independent component for displaying glycans and as an easy-to-use drawing tool. The "GlycanBuilder" can be integrated in web pages as a Java applet for the visual editing of glycans. The same component is available as a web service to render an encoded structure into a graphical format. Finally, the "GlycanBuilder" can be integrated into other applications to create intuitive and appealing user interfaces: an example is the "GlycoWorkbench", a software tool for assisted annotation of glycan mass spectra. The "GlycanBuilder" represent a flexible, reliable and efficient solution to the problem of input and output of glycan structures in any glycomic tool or database.