search.glycans.by.name: Client-side interface to obtain a list of chemical glycans
In kozo2/keggapi: Client-side REST access KEGG

Description Usage Arguments Details Value Author(s) References See Also Examples

View source: R/KEGGREST.R

The functions provide access to KEGG LIGAND database http://www.genome.jp/kegg/ligand.html. Given a glycan name, a composition, a molecular weight, or a common sub-structure, one of the functions below can return a list of glycans identifiers from KEGG LIGAND database.

search.glycans.by.name(name)
search.glycans.by.composition(composition)
search.glycans.by.mass(mass, range)
search.glycans.by.kcam(kcf, program, option, offset, limit)

`name`	`name` a character string to indicate a glycan name
`composition`	`composition` a character string to indicate the composition of monosaccharides
`mass`	`mass` a float to indicate the mass computed from the composition, excluding those in parentheses
`range`	`range` a float to indicate the range of molecular weight when searching glycans by mass
`kcf`	`kcf` a character string to indicate the molecular structure (carbohydrate sequence) of a glycan in KCF format
`program`	`program` a character string, either "gapped" or "ungaped"
`option`	`option` a character string, either "global" or "local"
`offset`	`offset` an integer
`limit`	`limit` an integer

search.glycans.by.name returns a list of glycans having the specified name;

search.glycans.by.composition returns a list of glycans containing sugars indicated by the composition. Order of the sugars (in parenthesis with number) is insensitive;

search.glycans.by.mass returns a list of glycans having the molecular weight around "mass" with some ambiguity (range);

search.glycans.by.subcomp returns a list of glycans with the alignment having common sub-structure calculated by the KCaM program. You can obtain a KCF formatted structural data of matched glycans using bget with the "-f m" option to confirm the alignment.

All the functions return a character vector of glycan identifiers provided by KEGG LIGAND database

Kozo Nishida

http://www.kegg.jp/kegg/docs/keggapi.html

bget

	glycans_1 <- search.glycans.by.name("Paragloboside")
        glycans_2 <- search.glycans.by.composition("(Man)4 (GalNAc)1")
        glycans_3 <- search.glycans.by.mass(689.6, 0.1)
        kcf <- bget("-f k gl:G12922")
        glycans_4 <- search.glycans.by.kcam(kcf, "gapped", "local", 1, 5)