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glymotif

The goal of glymotif is to extract glycan motifs from glycan structures. It works seemlessly with glyrepr and glyparse.

Installation

You can install the development version of glymotif from GitHub with:

# install.packages("pak")
pak::pak("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

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