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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 GlyGen Collection, 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. The package seamlessly integrates with the glycoverse ecosystem, particularly ‘glyrepr’ and ‘glyparse’, making it essential for structural glycomics analysis, biomarker discovery, and understanding glycan-mediated biological processes.

Installation

Install glycoverse

We recommend installing the meta-package glycoverse, which includes this package and other core glycoverse packages.

Install glymotif alone

If you don’t want to install all glycoverse packages, you can only install glymotif.

You can install the latest release of glymotif from r-universe (recommended):

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

Or from GitHub:

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

Or install the development version (NOT recommended):

pak::pkg_install("glycoverse/glymotif")

Note: Tips and troubleshooting for the meta-package glycoverse are also applicable here: Installation of glycoverse.

Documentation

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

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