Implementation of GlycanBuilder to draw a wide variety of ambiguous glycans
Implementation of GlycanBuilder to draw a wide variety of ambiguous glycans
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DOI：
10.1016/j.carres.2017.04.015
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发表时间：
2017-06-05
影响因子：
3.1
通讯作者：
Narimatsu, Hisashi
中科院分区：
文献类型：
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作者：
Tsuchiya, Shinichiro;Aoki, Nobuyuki P.;Narimatsu, Hisashi
GlyTouCan版本1.0作为国际糖链结构库于2015年发布，在GlyTouCan项目的早期阶段提出了一种名为WURCS(碳水化合物结构的Web3唯一表示)的新序列格式。GlyTouCan使用WURCS作为其多糖的基本表示，因为现有的格式在灵活性方面不足以通用地表示任何和所有的多糖。因此，为了获得用于现有或新的糖链结构的WURCS字符串，需要能够输出WURCS的转换工具或糖链结构编辑器。由于社区对GlycanBuilder的广泛使用，GlycanBuilder显然是扩展的选择。然而，GlycanBuilder是有限的，因为它最初是为了支持哺乳动物的多糖而开发的。它也不支持新提出的被称为多糖符号命名法(SNFG)的单糖符号标准。因此，在这项工作中，我们实现了一个新版本的GlycanBuilder，以极大地提高其可用性。重组了葡聚糖呈现系统，以便能够呈现环状多糖、嵌套重复单元、单糖组成和交联性多糖结构。还实现了WURCS的导入和导出实用程序，并加入了SNFG符号，以允许使用最新的多糖符号命名法将多糖导出为图形。这一新版本的GlycanBuilder名为“GlycanBuilder2”，能够支持各种不明确的多糖，包括含有细菌和植物的单糖的结构。这些多糖也可以使用新的SNFG符号来显示。这一工具可以帮助研究人员更快地就多糖的复杂、多样和模糊的结构进行沟通。此外，新的GlycanBuilder现在可以轻松地从画布上绘制的多糖输出WURCS序列。最重要的是，由于GlyTouCan使用WURCS作为注册和搜索多糖信息的基本格式，因此现在可以在GlyTouCan中轻松注册和查询更多种类的多糖。(C)2017年作者。爱思唯尔有限公司出版。
GlyTouCan version 1.0 was released in 2015 as the international glycan structure repository, and a new sequence format called WURCS (Web3 Unique Representation of Carbohydrate Structures) was proposed during the early stages of the GlyTouCan project. GlyTouCan uses WURCS as its base representation for glycans because existing formats were insufficient in their flexibility to represent any and all glycans universally. Therefore, in order to obtain WURCS strings for existing or new glycan structures, conversion tools or glycan structure editors that can export WURCS became necessary. GlycanBuilder was an obvious choice to extend due to its wide usage by the community. However, GlycanBuilder was limited because it was originally developed to support mammalian glycans. It also did not support the newly proposed monosaccharide symbol standard called Symbol Nomenclature for Glycans (SNFG). Therefore in this work, we implemented a new version of GlycanBuilder to greatly increase its usability. The glycan rendering system was refactored so that cyclic glycans, nested repeating, units, monosaccharide compositions and cross-linked glycan structures can be represented. Both import and export utilities for WURCS were also implemented and SNFG symbols were incorporated to allow glycans to be exported as graphics using the latest glycan symbol nomenclature.This new version of GlycanBuilder called "GlycanBuilder2", is able to support a wide variety of ambiguous glycans, including structures containing monosaccharides from bacteria and plants. These glycans can also be displayed using the new SNFG symbols. This tool can aid researchers in communicating about the complex, diverse, and ambiguous structures of glycans more rapidly. Moreover, the new GlycanBuilder can now easily output WURCS sequences from glycans drawn on the canvas. Most importantly, because GlyTouCan employs WURCS as the basic format for registration and searching of glycan information, a wider variety of glycans can now be readily registered and queried in GlyTouCan. (C) 2017 The Authors. Published by Elsevier Ltd.