Extract Glycan Motifs from Glycan Structures

Identify, count, and match recurring substructures in glycan structures. Supports concrete and generic monosaccharide matching, several structural alignment modes, node-to-node mappings, and batch analysis using subgraph isomorphism. Includes curated motif annotations derived from the 'GlycoMotif' resource < https://glycomotif.glyomics.org/>. Integrates with 'glyrepr' and 'glyparse' for structural glycomics workflows.

glymotif

Provides comprehensive tools for glycan motif analysis and detection in glycobioinformatics research. The package enables users to identify, count, and match glycan motifs (recurring substructures) within complex glycan structures using advanced subgraph isomorphism algorithms. It includes a curated database of known motifs from the GlycoMotif database, supports both concrete and generic monosaccharide matching, and offers flexible alignment options (core, terminal, or anywhere). Key functionalities include motif presence detection, occurrence counting, detailed node-to-node mapping, and batch analysis of multiple glycans against multiple motifs.

Installation

Once glymotif is available on CRAN, you can install the latest release from CRAN:

pak::pkg_install("glymotif")

Or from r-universe:

pak::repo_add(glycoverse = "https://glycoverse.r-universe.dev")
pak::pkg_install("glymotif")

Or install the latest GitHub release:

pak::pkg_install("glycoverse/glymotif@*release")

Or install the development version from GitHub:

pak::pkg_install("glycoverse/glymotif")

Documentation

• 🚀 Get started: Here
• 🔧 Motif matching rules: Here
• 📚 Reference: Here

Role in glycoverse

glymotif provides possibilities for one important job in glyco-bioinformatics: to detect motifs in glycans. The package is designed to be used directly by users for structural analysis, as well as to provide backend support for other packages in the glycoverse ecosystem.

Example

library(glymotif)
library(glyparse)

Say we have a glycan, …

(glycan <- parse_iupac_condensed("Gal(b1-3)GlcNAc(b1-3)Gal(b1-3)GalNAc(a1-"))
#> <glycan_structure[1]>
#> [1] Gal(b1-3)GlcNAc(b1-3)Gal(b1-3)GalNAc(a1-
#> # Unique structures: 1

… and we want to check if it has the O-Glycan core 1 motif.

have_motif(glycan, "Gal(b1-3)GalNAc(a1-", alignment = "core")
#> [1] TRUE

Or use the motif name directly.

have_motif(glycan, "O-Glycan core 1")
#> [1] TRUE