KCaM (KEGG Carbohydrate Matcher): a software tool for analyzing the structures of carbohydrate sugar chains
KCaM (KEGG Carbohydrate Matcher): a software tool for analyzing the structures of carbohydrate sugar chains
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DOI：
10.1093/nar/gkh473
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发表时间：
2004-07-01
影响因子：
14.9
通讯作者：
Kanehisa, M
中科院分区：
文献类型：
--
作者：
Aoki, KF;Yamaguchi, A;Kanehisa, M
KCaM（KEGG碳水化合物匹配器）是一种分析碳水化合物糖链或聚糖的工具。它包括一个基于Web的图形用户界面，允许用户使用鼠标轻松输入聚糖。然后将聚糖结构转换为我们的KCF（KEGG化学功能）文件格式，并发送到我们的程序中，该程序实现了有效的树结构比对算法，类似于序列比对算法，但用于分支树结构。用户还可以从本地计算机检索KCF格式的聚糖树结构，以便通过网络进行可视化。树匹配算法为对聚糖执行不同类型的树匹配程序提供了几个选项。这些选项包括是否在匹配中纳入差距，是否考虑到联系信息以及局部与全局的一致性。该程序的结果以基于这些选项的相似性顺序的聚糖结构列表的形式返回。实际的比对可以通过图形方式查看，注释信息也可以很容易地查看，因为所有这些信息都与KEGG的全面基因组数据套件相关联。类似于BLAST，用户因此能够使用各种树比对选项将感兴趣的聚糖结构与来自不同聚糖数据库的聚糖进行比较。KCaM目前可在http://glycan.genome.ad.jp上获得。
KCaM (KEGG Carbohydrate Matcher) is a tool for the analysis of carbohydrate sugar chains, or glycans. It consists of a web-based graphical user interface that allows users to enter glycans easily with the mouse. The glycan structure is then transformed into our KCF (KEGG Chemical Function) file format and sent to our program which implements an efficient tree-structure alignment algorithm, similar to sequence alignment algorithms but for branched tree structures. Users can also retrieve glycan tree structures in KCF format from their local computers for visualization over the web. The tree-matching algorithm provides several options for performing different types of tree-matching procedures on glycans. These options consist of whether to incorporate gaps in a match, whether to take the linkage information into consideration and local versus global alignment. The results of this program are returned as a list of glycan structures in order of similarity based on these options. The actual alignment can be viewed graphically, and the annotation information can also be viewed easily since all this information is linked with KEGG's comprehensive suite of genomic data. Analogously to BLAST, users are thus able to compare glycan structures of interest with glycans from different glycan databases using a variety of tree-alignment options. KCaM is currently available at http://glycan.genome.ad.jp.