Skip Navigation

UniCarbKB


NAR Molecular Biology Database Collection entry number 292
Packer, Nicolle; Campbell, Matthew; Peterson, Robyn; Mariethoz, Julien; Gasteiger, Elisabeth;
Proteome Systems Ltd., Locked Bag 2073, North Ryde, Sydney, NSW 1670, Australia.

Database Description

GlycoSuiteDB release 5, January 2003, contains more than 7800 annotated entries of glycan structures derived from glycoproteins, or free oligosaccharides isolated from biologically important fluids such as milk, saliva and urine. For each structure information is available concerning the glycan type, linkage and anomeric configuration, mass and composition. Detailed information is provided on native and recombinant sources, including species, tissue and/or cell type, cell line, strain, blood group and disease state. There are over 1000 different biological sources represented in GlycoSuiteDB, from over 200 different tissue or cell types. Where known, the proteins to which the glycan structures are attached are described, and cross- references to SWISS-PROT are given if applicable. The database annotations include literature references which are linked to PubMed. Detailed information on the methods used to determine each glycan structure are provided to help the user assess the quality of the structural assignment. The web site (http://www.glycosuite.com) allows the user to search the database using a combination of 2-D glycan structure, composition, glycan linkage type, reducing-terminal sugar residue, glycan mass (monoisotopic or average), species, biological system, tissue or cell type, disease state, protein name, SWISS-PROT/TrEMBL accession number, or reference information. Results can be sorted by glycan mass, protein name, tissue or cell type, disease state or taxonomy. The emphasis of this database is to be consistent. This will enable reliable mining of the information for future applications of glycobiology.

Recent Developments

An exciting new feature has been added to GlycoSuiteDB. We have now enabled searching by 2-D glycan structure. The user may construct a 2-D structure, or partial structure, via a simple point and click interface. Using a novel search method, this user-defined structure is matched with any part of a glycan structure in GlycoSuiteDB. This new search facility enables the user to rapidly and correctly identify glycan structures containing significant branching and specific epitopes that may be of biological importance. This 2-D glycan structure query may also be combined with any of the existing query types in an advanced query.

Acknowledgements

.

References

1. Cooper, C.A., Harrison, M.J., Wilkins, M.R., and Packer, N.H. (2001). GlycoSuiteDB: a new curated relational database of glycoprotein glycan structures and their biological sources. Nucleic Acids Res. 29; 332-335.
2. Cooper, C.A., Harrison, M.J., Webster, J.M., Wilkins, M.R., and Packer, N.H. (2002). Data standardisation in GlycoSuiteDB. Pac. Symp. Biocomputing 2002; 297-309.

Subcategory: Carbohydrates

Go to the abstract in the NAR 2014 Database Issue.
Oxford University Press is not responsible for the content of external internet sites