The GlycanBuilder and GlycoWorkbench glycoinformatics tools: updates and new developments

Abstract During the EUROCarbDB project our group developed the GlycanBuilder and GlycoWorkbench glycoinformatics tools. This short communication summarizes the capabilities of these two tools and updates which have been made since the original publications in 2007 and 2008. GlycanBuilder is a tool that allows for the fast and intuitive drawing of glycan structures; this tool can be used standalone, embedded in web pages and can also be integrated into other programs. GlycoWorkbench has been designed to semi-automatically annotate glycomics data. This tool can be used to annotate mass spectrometry (MS) and MS/MS spectra of free oligosaccharides, N and O-linked glycans, GAGs (glycosaminoglycans) and glycolipids, as well as MS spectra of glycoproteins.

[1]  R. Laine,et al.  A calculation of all possible oligosaccharide isomers both branched and linear yields 1.05 x 10(12) structures for a reducing hexasaccharide: the Isomer Barrier to development of single-method saccharide sequencing or synthesis systems. , 1994, Glycobiology.

[2]  R Apweiler,et al.  On the frequency of protein glycosylation, as deduced from analysis of the SWISS-PROT database. , 1999, Biochimica et biophysica acta.

[3]  C. W. von der Lieth,et al.  LINUCS: linear notation for unique description of carbohydrate sequences. , 2001, Carbohydrate research.

[4]  Chris F. Taylor,et al.  A common open representation of mass spectrometry data and its application to proteomics research , 2004, Nature Biotechnology.

[5]  B. Domon,et al.  A systematic nomenclature for carbohydrate fragmentations in FAB-MS/MS spectra of glycoconjugates , 1988, Glycoconjugate Journal.

[6]  Martin Frank,et al.  GLYCOSCIENCES.de: an Internet portal to support glycomics and glycobiology research. , 2006, Glycobiology.

[7]  Wei Lang,et al.  Advancing glycomics: implementation strategies at the consortium for functional glycomics. , 2006, Glycobiology.

[8]  Alessio Ceroni,et al.  The GlycanBuilder: a fast, intuitive and flexible software tool for building and displaying glycan structures , 2007, Source Code for Biology and Medicine.

[9]  Alessio Ceroni,et al.  GlycoWorkbench: a tool for the computer-assisted annotation of mass spectra of glycans. , 2008, Journal of proteome research.

[10]  Thomas Wetter,et al.  GlycomeDB – integration of open-access carbohydrate structure databases , 2008, BMC Bioinformatics.

[11]  Alessio Ceroni,et al.  Software tool for the structural determination of glycosaminoglycans by mass spectrometry. , 2008, Analytical chemistry.

[12]  J. Marth,et al.  A unified vision of the building blocks of life , 2008, Nature Cell Biology.

[13]  René Ranzinger,et al.  Statistical analysis of the Bacterial Carbohydrate Structure Data Base (BCSDB): Characteristics and diversity of bacterial carbohydrates in comparison with mammalian glycans , 2008, BMC Structural Biology.

[14]  C. Lieth,et al.  GlycoCT-a unifying sequence format for carbohydrates. , 2008, Carbohydrate research.

[15]  Martin Frank,et al.  Glycome-DB.org: a portal for querying across the digital world of carbohydrate sequences. , 2009, Glycobiology.

[16]  Louise Royle,et al.  Proposal for a standard system for drawing structural diagrams of N‐ and O‐linked carbohydrates and related compounds , 2009, Proteomics.

[17]  Richard D Cummings,et al.  Symbol nomenclature for glycan representation , 2009, Proteomics.

[18]  Lennart Martens,et al.  mzML—a Community Standard for Mass Spectrometry Data* , 2010, Molecular & Cellular Proteomics.

[19]  Pauline M Rudd,et al.  Symbol nomenclature for representing glycan structures: Extension to cover different carbohydrate types , 2011, Proteomics.

[20]  Martin Frank,et al.  EUROCarbDB: An open-access platform for glycoinformatics , 2010, Glycobiology.