Invalid GWS using Glycan.toString()

[ReneRanzinger]

Example GlyTouCan ID: G17689DH

Using the Glycan.toString() method: redEnd--?b?D-b-D-Glcp,p((--2NAc)--4b1D-b-D-Glcp,p(--2NAc)--4b1D-b-D-Manp,p(--3a1D-a-D-Manp,p--2b1D-b-D-Glcp,p(--2NAc)--4b1D-b-D-Galp,p--3a2D-a-D-Neup,p--5NAc)--6a1D-a-D-Manp,p--2b1D-b-D-Glcp,p(--2NAc)--4b1D-b-D-Galp,p--3a2D-a-D-Neup,p--5NAc)--6a1L-a-L-Fucp,p$MONO,perMe,Na,0,redEnd

But it should be: freeEnd--?b1D-GlcNAc,p(--4b1D-GlcNAc,p--4b1D-Man,p(--3a1D-Man,p--2b1D-GlcNAc,p--4b1D-Gal,p--3a2D-NeuAc,p)--6a1D-Man,p--2b1D-GlcNAc,p--4b1D-Gal,p--3a2D-NeuAc,p)--6a1L-Fuc,p$MONO,perMe,Na,0,freeEnd

The upper string is no longer compatible with GWB and will not load. Main issues are the replication of anomer, ring and configuration in residue name that prevent a matching and the separation of 2NAc from monosaccharides.

[e15d5605]

I tested a conversion functionality of GWS(GWB) format from WURCS using GlycanBuiler (1.12.0).

• Import string (WURCS)

  WURCS=2.0/6,12,11/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a2112h-1b_1-5][Aad21122h-2a_2-6_5*NCC/3=O][a1221m-1a_1-5]/1-1-2-3-1-4-5-3-1-4-5-6/a4-b1_a6-l1_b4-c1_c3-d1_c6-h1_d2-e1_e4-f1_f3-g2_h2-i1_i4-j1_j3-k2

• Export string (GWS)

  freeEnd--1b1D-GlcNAc,p(--4b1D-GlcNAc,p--4b1D-Man,p(--3a1D-Man,p--2b1D-GlcNAc,p--4b1D-Gal,p--3a2D-NeuAc,p)--6a1D-Man,p--2b1D-GlcNAc,p--4b1D-Gal,p--3a2D-NeuAc,p)--6a1L-Fuc,p$MONO,Und,0,0,freeEnd

I also entered GWS into GlycanBuilder2.\ As a result, the following glycan image was depict.

• Export image (from GWS)

Based on the above, I considered that this problem was resolved in the latest version of GlycanBuilder2 (1.12.0).

[edwardsnj]

Actually, the issue is (based on some experimenting just now), that if you use org.glycoinfo.application.glycanbuilder.converterWURCS2.WURCS2Parser and WURCS sequence to construct the glycan, you get correctly formatted GWB sequence, but if you use org.eurocarbdb.application.glycanbuilder.converterGlycoCT.GlycoCTCondensedParse and GlycoCT sequence to construct the glycan, you get incorrectly formatted GWB sequence.

The sequences I used were from here: https://glycans.glyomics.org/glycandata/G17689DH

Any insight?

Why would GlycoCT-based glycan generate different GWB format sequence?

Thanks,

• n