Using the KEGG database resource.

KEGG (Kyoto Encyclopedia of Genes and Genomes) is a bioinformatics resource for understanding the functions and utilities of cells and organisms from both high-level and genomic perspectives. It is a self-sufficient, integrated resource consisting of genomic, chemical, and network information, with cross-references to numerous outside databases, containing a complete set of building blocks (genes and molecules) and wiring diagrams (interaction networks) to represent cellular functions. This unit describes protocols for using KEGG, KEGG PATHWAY, KEGG GENES, KEGG SSDB, KEGG EXPRESSION, and KEGG LIGAND.

Efficient tree-matching methods for accurate carbohydrate database queries.

One aspect of glycome informatics is the analysis of carbohydrate sugar chains, or glycans, whose basic structure is not a sequence, but a tree structure. Although there has been much work in the development of sequence databases and matching algorithms for sequences (for performing queries and analyzing similarity), the more complicated tree structure of glycans does not allow a direct implementation of such a database for glycans, and further, does not allow for the direct application of sequence alignment algorithms for performing searches or analyzing similarity. Therefore, we have utilized a polynomial-time dynamic programming algorithm for solving the maximum common subtree of two trees to implement an accurate and efficient tool for finding and aligning maximally matching glycan trees.

A score matrix to reveal the hidden links in glycans.

Motivation: Glycans are the third major class of biomolecules following DNA and proteins. They are extremely vital for the functioning of multicellular organisms. However, comparing the fast development of sequence analysis techniques, informatics work on glycans have a long way to go.

The evolutionary repertoires of the eukaryotic-type ABC transporters in terms of the phylogeny of ATP-binding domains in eukaryotes and prokaryotes.

ABC (ATP-binding cassette) transporters play an important role in the communication of various substrates across cell membranes. They are ubiquitous in prokaryotes and eukaryotes, and eukaryotic types (EK-types) are distinguished from prokaryotic types (PK-types) in terms of their genes and domain organizations. The EK-types and PK-types mainly consist of exporters and importers, respectively.

Application of a new probabilistic model for recognizing complex patterns in glycans.

Motivation: The study of carbohydrate sugar chains, or glycans, has been one of slow progress mainly due to the difficulty in establishing standard methods for analyzing their structures and biosynthesis. Glycans are generally tree structures that are more complex than linear DNA or protein sequences, and evidence shows that patterns in glycans may be present that spread across siblings and into further regions that are not limited by the edges in the actual tree structure itself. Current models were not able to capture such patterns.

KCaM (KEGG Carbohydrate Matcher): a software tool for analyzing the structures of carbohydrate sugar chains.

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.