Implementation of GlycanBuilder to draw a wide variety of ambiguous glycans

Shinichiro Tsuchiya; Nobuyuki P Aoki; Daisuke Shinmachi; Masaaki Matsubara; Issaku Yamada; Kiyoko F Aoki-Kinoshita; Hisashi Narimatsu

doi:10.1016/j.carres.2017.04.015

Implementation of GlycanBuilder to draw a wide variety of ambiguous glycans

Carbohydr Res. 2017 Jun 5:445:104-116. doi: 10.1016/j.carres.2017.04.015. Epub 2017 Apr 19.

Authors

Shinichiro Tsuchiya¹, Nobuyuki P Aoki², Daisuke Shinmachi², Masaaki Matsubara³, Issaku Yamada³, Kiyoko F Aoki-Kinoshita⁴, Hisashi Narimatsu⁵

Affiliations

¹ Graduate School of Engineering, Soka University, Tokyo, Japan.
² Faculty of Science and Engineering, Soka University, Tokyo, Japan.
³ The Noguchi Institute, Tokyo, Japan.
⁴ Graduate School of Engineering, Soka University, Tokyo, Japan; Faculty of Science and Engineering, Soka University, Tokyo, Japan; Glycoscience and Glycotechnology Research Group, AIST, Tsukuba, Japan. Electronic address: kkiyoko@soka.ac.jp.
⁵ Glycoscience and Glycotechnology Research Group, AIST, Tsukuba, Japan.

PMID: 28525772
DOI: 10.1016/j.carres.2017.04.015

Abstract

GlyTouCan version 1.0 was released in 2015 as the international glycan structure repository, and a new sequence format called WURCS (Web3 Unique Representation of Carbohydrate Structures) was proposed during the early stages of the GlyTouCan project. GlyTouCan uses WURCS as its base representation for glycans because existing formats were insufficient in their flexibility to represent any and all glycans universally. Therefore, in order to obtain WURCS strings for existing or new glycan structures, conversion tools or glycan structure editors that can export WURCS became necessary. GlycanBuilder was an obvious choice to extend due to its wide usage by the community. However, GlycanBuilder was limited because it was originally developed to support mammalian glycans. It also did not support the newly proposed monosaccharide symbol standard called Symbol Nomenclature for Glycans (SNFG). Therefore in this work, we implemented a new version of GlycanBuilder to greatly increase its usability. The glycan rendering system was refactored so that cyclic glycans, nested repeating units, monosaccharide compositions and cross-linked glycan structures can be represented. Both import and export utilities for WURCS were also implemented and SNFG symbols were incorporated to allow glycans to be exported as graphics using the latest glycan symbol nomenclature. This new version of GlycanBuilder called "GlycanBuilder2", is able to support a wide variety of ambiguous glycans, including structures containing monosaccharides from bacteria and plants. These glycans can also be displayed using the new SNFG symbols. This tool can aid researchers in communicating about the complex, diverse, and ambiguous structures of glycans more rapidly. Moreover, the new GlycanBuilder can now easily output WURCS sequences from glycans drawn on the canvas. Most importantly, because GlyTouCan employs WURCS as the basic format for registration and searching of glycan information, a wider variety of glycans can now be readily registered and queried in GlyTouCan.

Keywords: Glycan sequence format; Glycan visualization; Glyco bioinformatics; Sequence conversion; Symbolic notation.

MeSH terms

Carbohydrate Sequence
Computer Graphics
Glycomics / methods*
Polysaccharides / chemistry*

Substances

Polysaccharides