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The increasing amount of genomic and molecular information is the basis for understanding higher-order biological systems, such as the cell and the organism, and their interactions with the environment, as well as for medical, industrial and other practical applications. The KEGG resource (http://www.genome.jp/kegg/) provides a reference knowledge base for(More)
KEGG is a database resource (http://www.genome.jp/kegg/) that provides all knowledge about genomes and their relationships to biological systems such as cells and whole organisms as well as their interactions with the environment. KEGG is categorized in terms of building blocks in the genomic space, known as KEGG GENES, the chemical space, KEGG LIGAND, as(More)
Bioinformatics approaches to carbohydrate research have recently begun using large amounts of protein and carbohydrate data. In this field called glycome informatics, the foremost necessity is a comprehensive resource for genome-scale bioinformatics analysis of glycan data. Although the accumulation of experimental data may be useful as a reference of(More)
Mining frequent patterns is a general and important issue in data mining. Complex and unstructured (or semi-structured) datasets have appeared in major data mining applications, including text mining, web mining and bioinformatics. Mining patterns from these datasets is the focus of many of the current data mining approaches. We focus on labeled ordered(More)
Key issues relating to glycomics research were discussed after the workshop entitled "Frontiers in Glycomics: Bioinformatics and Biomarkers in Disease" by two focus groups nominated by the organizers. The groups focused on two themes: (i) glycomics as the new frontier for the discovery of biomarkers of disease and (ii) requirements for the development of(More)
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(More)
Glycans are known as the third major class of biopolymers, next to DNA and proteins. They cover the surfaces of many cells, serving as the 'face' of cells, whereby other biomolecules and viruses interact. The structure of glycans, however, differs greatly from DNA and proteins in that they are branched, as opposed to linear sequences of amino acids or(More)
Glycans, or carbohydrate sugar chains, which play a number of important roles in the development and functioning of multicellular organisms, can be regarded as labeled ordered trees. A recent increase in the documentation of glycan structures, especially in the form of database curation, has made mining glycans important for the understanding of living(More)
This chapter describes the Glycan Miner Tool, which is available as a part of the Resource for INformatics of Glycomes at Soka Web site. It implements the α-closed frequent subtree algorithm to find significant subtrees from within a data set of glycan structures, or carbohydrate sugar chains. The results are returned in order of p-value, which is computed(More)