An Introduction to Bioinformatics for Glycomics Research

Carbohydrates are considered the thirdclass of information-encoding biologicalmacromolecules. ‘‘Glycomics,’’ the scientificattempt to characterize and study carbohy-drates, is a rapidly emerging branch ofscience, for which informatics is just begin-ning. Glycomics requires sophisticated algo-rithmic approaches. Several algorithms andmodels have been developed for glycobiol-ogy research in the past several years. Thistutorial will provide a brief introduction tothe field of glycome informatics, which willinclude a primer on glycobiology as well asdescriptions of the algorithms and modelsthat have been developed in this field.The four essential molecular buildingblocks of cells are nucleic acids, proteins,lipids, and carbohydrates, often referred toas glycans. Nucleotide and protein sequenc-es are at the heart of nearly all bioinfor-matics applications and research, whereasglycan and lipid structures have been widelyneglected in bioinformatics. However, gly-cans are the most abundant and structurallydiverse biopolymers formed in nature.Bound to proteins, as glycoproteins, theyare known to affectthefunctions of proteins.More than half of all protein sequencesdeposited in the SWISS-PROT databankinclude potential glycosylation sites and thusmay be glycoproteins. Based on an analysisof well-annotated and characterized glyco-proteins inSWISS-PROT,itwas concludedthat more than half of all proteins areglycosylated [1].The development and use of informaticstools and databases for glycobiology andglycomics research has increased consider-ably in recent years. However, the generaldevelopment in this field can still beconsidered as being in its infancy whencompared to the genomics and proteomicsareas. In terms of bioinformatics in glyco-biology, there are several paths of researchthat are currently in progress. The develop-ment of algorithms to reliably support thecharacterization of glycan structures forhigh-throughput applications is the mostimmediate demand of the glycomics com-munity. Additionally, several major glyco-related projects (Consortium for FunctionalGlycomics [2], KEGG Glycan [3], GLY-COSCIENCES.de [4]) are maturing andprovide well-structured glyco-related datathat are awaiting data mining and analysis.With the exciting new developments incarbohydrate arrays and automated MSannotation, the analysis of the glycome hasreached a new level of sophistication, whichrequires broader informatics support. Thistutorial aims to give an overview of thecurrent status of carbohydrate databases, thenewest analytical techniques, as well as theinformatics needed for rapid progress inglycomics research.