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Parsing glycan structure text representations.
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glycoverse/glyparse
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Parse different glycan structure text nomenclature intoglyrepr::glycan_structure.
Currently, the following formats are supported: IUPAC-extended,IUPAC-condensed, IUPAC-short, WURCS, GlycoCT, StrucGP-style,pGlyco-style.
You can install the latest release of glyparse from CRAN with:
install.packages("glyparse")Or install the development version from GitHub:
remotes::install_github("glycoverse/glyparse")
- 📚 Reference:Here
Whileglyrepr natively supports parsing IUPAC-condensed format throughas_glycan_structure(), the glycan community has developed numerousother nomenclature formats that remain widely adopted in differentcontexts.glyparse serves as a comprehensive extension toglyrepr,providing robust parsing capabilities for these diverse formats. Thepackage can be utilized directly by researchers to parse glycanstructure text strings, or integrated with other packages such asglyread to seamlessly handle structure parsing when processing resultsfrom glycan and glycopeptide analysis software.
library(glyparse)# Parse a StrucGP-style structure stringparse_strucgp_struc("A2B2C1D1E2F1fedD1E2edcbB5ba")#> <glycan_structure[1]>#> [1] Hex(??-?)HexNAc(??-?)Hex(??-?)[HexNAc(??-?)Hex(??-?)]Hex(??-?)HexNAc(??-?)[dHex(??-?)]HexNAc(??-#> # Unique structures: 1
# Parse a pGlyco-style structure stringparse_pglyco_struc("(N(F)(N(H(H(N))(H(N(H))))))")#> <glycan_structure[1]>#> [1] Hex(??-?)HexNAc(??-?)Hex(??-?)[HexNAc(??-?)Hex(??-?)]Hex(??-?)HexNAc(??-?)[dHex(??-?)]HexNAc(??-#> # Unique structures: 1
# Parse a condensed IUPAC structure stringparse_iupac_condensed("Gal(b1-3)GlcNAc(b1-4)Glc(a1-")#> <glycan_structure[1]>#> [1] Gal(b1-3)GlcNAc(b1-4)Glc(a1-#> # Unique structures: 1
# Parse a WURCS structure stringparse_wurcs("WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3/a4-b1_b4-c1_c3-d1_c6-e1")#> <glycan_structure[1]>#> [1] Man(a1-3)[Man(a1-6)]Man(b1-4)GlcNAc(b1-4)GlcNAc(b1-#> # Unique structures: 1
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