Find a Virtual Biosynthesis Path Between Glycan Structures
path_biosynthesis_virtual.RdInfer every structure-driven biosynthetic path from from to to by
trimming terminal residues and sulfate groups from to backward to from.
Unlike path_biosynthesis(), this does not require known enzyme rules.
Arguments
- from
A
glyrepr::glycan_structure()scalar, or a character string supported byglyparse::auto_parse(). The starting glycan structure.- to
A
glyrepr::glycan_structure()scalar, or a character string supported byglyparse::auto_parse(). The target glycan structure.- enzymes
A character vector of gene symbols, or a list of
enzyme()objects. Used only whenannotate_enzymesisTRUE; ifNULL, all available enzymes are considered.- annotate_enzymes
Whether to annotate each virtual transition with concrete enzymes whose rules can perform it. Defaults to
FALSE.
Value
A glyenzy_virtual_biosynthesis_network object inheriting from
glyenzy_biosynthesis_network and igraph::igraph(). Vertices contain
IUPAC-condensed strings in name; edges have a forward step and
virtual-enzyme enzyme attribute. When annotate_enzymes is TRUE,
concrete_enzymes is a list of character vectors containing every candidate
concrete enzyme for each transition.
Virtual enzymes
Each edge is named for the residue added by that step. Intact glycans include
the linkage anomer and acceptor position, so a beta-1,4-linked GlcNAc is
labeled "b4GlcNAcT". Partial and topological glycans omit linkage
information and use "GlcNAcT". Generic or mixed topological glycans use
their preserved generic residue names, such as "HexNAcT".
Sulfation is represented as its own atomic transition. Sulfate additions at
positions 3 and 6 use "3SulfoT" and "6SulfoT"; an unknown or other
position uses "?SulfoT". A sulfated terminal residue is therefore
desulfated before the residue itself can be trimmed.
Virtual tracing starts N-glycans at the N-glycan core and all other glycans
at their reducing-end root residue. Sulfates are removed from these
automatically selected starts. In path_biosynthesis_virtual(), the
explicit from glycan is always the virtual starting structure, including
any sulfate groups it contains; those sulfates must also occur in to.
These networks represent structural possibilities rather than biological
feasibility.
Generic structures do not retain glycan-class metadata. A generic structure
matching the N-glycan-core topology is therefore assumed to be an N-glycan;
use path_biosynthesis_virtual() with an explicit from when that topology
belongs to another glycan class.