Extract Branch Motifs

An N-glycan branching motif if the substructures linked to either the a3- or a6-core-mannose.

For example:

Neu5Ac - Gal - GlcNAc - Man
~~~~~~~~~~~~~~~~~~~~~      \
  A branching motif         Man - GlcNAc - GlcNAc -
                           /
                        Man

This function returns all the unique branching motifs found in the input glycans. It is very useful for analyzing N-glycan antennary patterns combined with glydet::quantify_motifs(). When used with have_motif() or related functions, we recommend setting alignment to "exact".

Usage

extract_branch_motif(glycans)

Arguments

glycans

One of:

• A glyrepr::glycan_structure() vector.

• A glycan structure string vector. All formats supported by glyparse::auto_parse() are accepted.

Value

A glyrepr::glycan_structure() vector containing the unique extracted branching motifs.

Details

The function works by:

1. Converting the input to a set of unique glycan_structure objects.

2. Searching for the N-glycan branch pattern: HexNAc(??-?)Hex(??-?)Hex(??-?)HexNAc(??-?)HexNAc(??-.

3. For each match, identifying the root node of the branch (the leftmost HexNAc in the pattern).

4. Extracting the full subtree rooted at that node.

5. Preserving the correct anomeric configuration (e.g., "b1") by inspecting the linkage to the root node.

Examples

glycans <- c(
  "Neu5Ac(a2-3)Gal(b1-4)GlcNAc(b1-2)Man(a1-3)[Man(a1-6)]Man(b1-4)GlcNAc(a1-4)GlcNAc(b1-",
  "Gal(b1-4)GlcNAc(b1-2)Man(a1-3)[Man(a1-6)]Man(b1-4)GlcNAc(a1-4)GlcNAc(b1-"
)
extract_branch_motif(glycans)
#> <glycan_structure[2]>
#> [1] Neu5Ac(a2-3)Gal(b1-4)GlcNAc(b1-
#> [2] Gal(b1-4)GlcNAc(b1-
#> # Unique structures: 2