KCaM

KCaM performs structural analysis and comparison of glycan (branched carbohydrate) structures by converting glycans into the KEGG Chemical Function (KCF) file format and applying tree-structure alignment algorithms to identify and rank similar structures.

Key Features:

• KCF conversion and I/O: Converts glycans into the KEGG Chemical Function (KCF) file format and supports KCF-formatted glycan tree input.
• Tree-structure alignment algorithm: Implements an efficient tree-structure alignment algorithm adapted for the branched topology of glycans.
• Alignment options: Supports gap incorporation, linkage consideration, and choices between local and global alignments.
• Similarity scoring and ranking: Produces ranked lists of similar glycan structures based on alignment results and user-defined parameters.
• Cross-database comparison: Enables comparison of glycan structures across different databases using diverse tree-alignment options.
• KEGG integration: Links glycan analysis results to KEGG genomic and annotation data for contextual interpretation.

Scientific Applications:

• Glycan structural comparison: Identifies conserved and divergent motifs within branched glycan structures.
• Similarity-based database search: Searches and ranks glycans from databases based on structural similarity.
• Functional annotation integration: Associates glycan structural similarity with KEGG genomic annotations to aid functional interpretation.
• Comparative glycomics: Compares glycan repertoires across datasets or databases to support comparative studies.

Methodology:

Glycans are converted to the KEGG Chemical Function (KCF) file format and analyzed using a tree-structure alignment algorithm tailored for branched glycans, with options for gap incorporation, linkage consideration, local/global alignments, and generation of ranked similarity lists; results can be linked to KEGG annotations.