LINUCS:: LInear Notation for Unique Description of Carbohydrate Sequences
LINUCS:: LInear Notation for Unique Description of Carbohydrate Sequences
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DOI：
10.1016/s0008-6215(01)00230-0
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发表时间：
2001-11-01
影响因子：
3.1
通讯作者：
von der Lieth, CW
中科院分区：
文献类型：
--
作者：
Bohne-Lang, A;Lang, E;von der Lieth, CW
蛋白质组学数据库的使用已成为分子生物学家日常工作中不可或缺的一部分，但这种情况尚未在碳水化合物的应用中实现。一个明显的原因是现有的数据集合很少被注释，并且不存在与其他资源的交叉链接。普遍接受的线性、规范的碳水化合物描述的存在，可以很容易地被计算机处理，将通过作为唯一的、明确的数据库访问键，实现分布式碳水化合物数据收集的有效自动交联。讨论了派生正则符号的各种可能性。它们可以分为单独需要结构描述的尝试和从结构中存在的首选图形方向（从非还原到还原端）的事实中获利的替代。为了在糖科学家之间展开富有成效的讨论，提出了一种可能的解决方案，其中选择还原单糖单元作为图根，并使用链接信息来定义各个分支的优先级。已经创建了一个Web界面（http://www.dkfz.de/spec/linucs/），它直接将复杂碳水化合物的常用扩展表示形式转换为首选的规范描述或其反向形式。2001爱思唯尔科学有限公司版权所有。
The use of proteomics databases has become indispensable for daily work of molecular biologists, but this situation has not yet been achieved for carbohydrate applications. One obvious reason is that existing data collections are only rarely annotated and no cross-linking to other resources exists. The existence of a generally accepted linear, canonical description for carbohydrates which can be readily processed by computers will enable efficient automatic cross-linking of distributed carbohydrate data collections by serving as a unique and unambiguous database access key. Various possibilities to derive a canonical notation are discussed. They can be divided into attempts that require structure description alone and alternatives that profit from the fact that a preferred graph direction (non-reducing to reducing end) exists within the structure. To open a fruitful discussion among glycoscientists a possible solution is presented where the reducing monosaccharide unit is selected as graph root and linkage information is used to define the priority of the various branches. A Web interface (http://www.dkfz.de/spec/linucs/) has been created that directly converts the commonly used extended representation of complex carbohydrates into the preferred canonical description or into its inverted form. (C) 2001 Elsevier Science Ltd. All rights reserved.