SugarSketcher is an intuitive and fast JavaScript interface module for online drawing of glycan structures in the popular Symbol Nomenclature for Glycans (SNFG) notation and exporting them to various commonly used formats encoding carbohydrate sequences (e.g., GlycoCT) or quality images (e.g., svg). It does not require a backend server or any specific browser plugins and can be integrated in any web glycoinformatics project. SugarSketcher allows drawing glycans both for glycobiologists and non-expert users. The "quick mode" allows a newcomer to build up a glycan structure having only a limited knowledge in carbohydrate chemistry. The "normal mode" integrates advanced options which enable glycobiologists to tailor complex carbohydrate structures. The source code is freely available on GitHub and glycoinformaticians are encouraged to participate in the development process while users are invited to test a prototype available on the ExPASY web-site and send feedback.

CEITEC⁻Central European Institute of Technology Masaryk University Brno 625 00 Brno Bohunice Czech Republic

Computer Science Department University of Geneva 1211 Geneva Switzerland

National Centre for Biomolecular Research Faculty of Science 625 00 Brno Bohunice Czech Republic

Polytech Nice Sophia Campus SophiaTech 06903 Sophia Antipolis France

Proteome Informatics Group SIB Swiss Institute of Bioinformatics 1211 Geneva Switzerland

Section of Biology University of Geneva 1211 Geneva Switzerland

Zelinsky Institute of Organic Chemistry Russian Academy of Sciences Laboratory of Carbohydrate Chemistry 119991 Moscow Russia

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Li E., Tabas I., Kornfeld S. The synthesis of complex-type oligosaccharides. I. Structure of the lipid-linked oligosaccharide precursor of the complex-type oligosaccharides of the vesicular stomatitis virus G protein. J. Biol. Chem. 1978;253:7762–7770. PubMed

Campbell M.P., Ranzinger R., Lütteke T., Mariethoz J., Hayes C.A., Zhang J., Akune Y., Aoki-Kinoshita K.F., Damerell D., Carta G., et al. Toolboxes for a standardised and systematic study of glycans. BMC Bioinform. 2014;15:S9. doi: 10.1186/1471-2105-15-S1-S9. PubMed DOI PMC

Varki A., Cummings R.D., Aebi M., Packer N.H., Seeberger P.H., Esko J.D., Stanley P., Hart G., Darvill A., Kinoshita T., et al. Symbol Nomenclature for Graphical Representations of Glycans. Glycobiology. 2015;25:1323–1324. doi: 10.1093/glycob/cwv091. PubMed DOI PMC

Cooper C.A., Joshi H.J., Harrison M.J., Wilkins M.R., Packer N.H. GlycoSuiteDB: A curated relational database of glycoprotein glycan structures and their biological sources. 2003 update. Nucleic Acids Res. 2003;31:511–513. doi: 10.1093/nar/gkg099. PubMed DOI PMC

Doubet S., Bock K., Smith D., Darvill A., Albersheim P. The Complex Carbohydrate Structure Database. Trends Biochem. Sci. 1989;14:475–477. doi: 10.1016/0968-0004(89)90175-8. PubMed DOI

Hashimoto K., Goto S., Kawano S., Aoki-Kinoshita K.F., Ueda N., Hamajima M., Kawasaki T., Kanehisa M. KEGG as a glycome informatics resource. Glycobiology. 2006;16:63R–70R. doi: 10.1093/glycob/cwj010. PubMed DOI

Ceroni A., Dell A., Haslam S.M. The GlycanBuilder: A fast, intuitive and flexible software tool for building and displaying glycan structures. Source Code Biol. Med. 2007;2:3. doi: 10.1186/1751-0473-2-3. PubMed DOI PMC

Von der Lieth C.-W., Freire A.A., Blank D., Campbell M.P., Ceroni A., Damerell D.R., Dell A., Dwek R.A., Ernst B., Fogh R., et al. EUROCarbDB: An open-access platform for glycoinformatics. Glycobiology. 2011;21:493–502. doi: 10.1093/glycob/cwq188. PubMed DOI PMC

Varki A., Cummings R.D., Esko J.D., Stanley P., Hart G.W., Aebi M., Darvill A.G., Kinoshita T., Packer N.H., Prestegard J.H., et al., editors. Essentials of Glycobiology. 3rd ed. Cold Spring Harbor Laboratory Press; Cold Spring Harbor, NY, USA: 2015. PubMed

Tsuchiya S., Aoki N.P., Shinmachi D., Matsubara M., Yamada I., Aoki-Kinoshita K.F., Narimatsu H. Implementation of GlycanBuilder to draw a wide variety of ambiguous glycans. Carbohydr. Res. 2017;445:104–116. doi: 10.1016/j.carres.2017.04.015. PubMed DOI

Joshi H.J., von der Lieth C.-W., Packer N.H., Wilkins M.R. GlycoViewer: A tool for visual summary and comparative analysis of the glycome. Nucleic Acids Res. 2010;38:W667–W670. doi: 10.1093/nar/gkq446. PubMed DOI PMC

Engelsen S.B., Hansen P.I., Pérez S. POLYS 2.0: An open source software package for building three-dimensional structures of polysaccharides: The POLYSaccharide Builder 2.0. Biopolymers. 2014;101:733–743. doi: 10.1002/bip.22449. PubMed DOI

Cheng K., Zhou Y., Neelamegham S. DrawGlycan-SNFG: A robust tool to render glycans and glycopeptides with fragmentation information. Glycobiology. 2016;27:200–205. doi: 10.1093/glycob/cww115. PubMed DOI PMC

Pérez S., Sarkar A., Rivet A., Breton C., Imberty A. Glyco3D: A Portal for Structural Glycosciences. In: Lütteke T., Frank M., editors. Glycoinformatics. Volume 1273. Springer; New York, NY, USA: 2015. pp. 241–258. PubMed

Sharon N. IUPAC-IUB Joint Commission on Biochemical Nomenclature (JCBN). Nomenclature of glycoproteins, glycopeptides and peptidoglycans: JCBN recommendations 1985. Glycoconj. J. 1986;3:123–133. doi: 10.1007/BF01049370. PubMed DOI

Toukach P.V., Egorova K.S. Carbohydrate structure database merged from bacterial, archaeal, plant and fungal parts. Nucleic Acids Res. 2016;44:D1229–D1236. doi: 10.1093/nar/gkv840. PubMed DOI PMC

Herget S., Ranzinger R., Maass K., Lieth C.-W.v.d. GlycoCT—A unifying sequence format for carbohydrates. Carbohydr. Res. 2008;343:2162–2171. doi: 10.1016/j.carres.2008.03.011. PubMed DOI

Mariethoz J., Alocci D., Gastaldello A., Horlacher O., Gasteiger E., Rojas-Macias M., Karlsson N.G., Packer N.H., Lisacek F. Glycomics@ExPASy: Bridging the Gap. Mol. Cell. Proteom. 2018;17:2164–2176. doi: 10.1074/mcp.RA118.000799. PubMed DOI PMC

Herget S., Toukach P.V., Ranzinger R., Hull W.E., Knirel Y.A., von der Lieth C.-W. Statistical analysis of the Bacterial Carbohydrate Structure Data Base (BCSDB): Characteristics and diversity of bacterial carbohydrates in comparison with mammalian glycans. BMC Struct. Biol. 2008;8:35. doi: 10.1186/1472-6807-8-35. PubMed DOI PMC

Harvey D.J., Merry A.H., Royle L., Campbell M.P., Dwek R.A., Rudd P.M. Proposal for a standard system for drawing structural diagrams of N- and O-linked carbohydrates and related compounds. Proteomics. 2009;9:3796–3801. doi: 10.1002/pmic.200900096. PubMed DOI

Horlacher O., Nikitin F., Alocci D., Mariethoz J., Müller M., Lisacek F. MzJava: An open source library for mass spectrometry data processing. J. Proteom. 2015;129:63–70. doi: 10.1016/j.jprot.2015.06.013. PubMed DOI

Kim S., Chen J., Cheng T., Gindulyte A., He J., He S., Li Q., Shoemaker B.A., Thiessen P.A., Yu B., et al. PubChem 2019 update: Improved access to chemical data. Nucleic Acids Res. 2018 doi: 10.1093/nar/gky1033. PubMed DOI PMC

Hastings J., Owen G., Dekker A., Ennis M., Kale N., Muthukrishnan V., Turner S., Swainston N., Mendes P., Steinbeck C. ChEBI in 2016: Improved services and an expanding collection of metabolites. Nucleic Acids Res. 2016;44:D1214–D1219. doi: 10.1093/nar/gkv1031. PubMed DOI PMC

Gotz L., Abrahams J.L., Mariethoz J., Rudd P.M., Karlsson N.G., Packer N.H., Campbell M.P., Lisacek F. GlycoDigest: A tool for the targeted use of exoglycosidase digestions in glycan structure determination. Bioinformatics. 2014;30:3131–3133. doi: 10.1093/bioinformatics/btu425. PubMed DOI PMC

Tiemeyer M., Aoki K., Paulson J., Cummings R.D., York W.S., Karlsson N.G., Lisacek F., Packer N.H., Campbell M.P., Aoki N.P., et al. GlyTouCan: An accessible glycan structure repository. Glycobiology. 2017;27:915–919. doi: 10.1093/glycob/cwx066. PubMed DOI PMC