An Introduction to Bioinformatics for Glycomics Research

Carbohydrates are considered the third class of information-encoding biological macromolecules. ‘‘Glycomics,’’ the scientific attempt to characterize and study carbohydrates, is a rapidly emerging branch of science, for which informatics is just beginning. Glycomics requires sophisticated algorithmic approaches. Several algorithms and models have been developed for glycobiology research in the past several years. This tutorial will provide a brief introduction to the field of glycome informatics, which will include a primer on glycobiology as well as descriptions of the algorithms and models that have been developed in this field. The four essential molecular building blocks of cells are nucleic acids, proteins, lipids, and carbohydrates, often referred to as glycans. Nucleotide and protein sequences are at the heart of nearly all bioinformatics applications and research, whereas glycan and lipid structures have been widely neglected in bioinformatics. However, glycans are the most abundant and structurally diverse biopolymers formed in nature. Bound to proteins, as glycoproteins, they are known to affect the functions of proteins. More than half of all protein sequences deposited in the SWISS-PROT databank include potential glycosylation sites and thus may be glycoproteins. Based on an analysis of well-annotated and characterized glycoproteins in SWISS-PROT, it was concluded that more than half of all proteins are glycosylated [1]. The development and use of informatics tools and databases for glycobiology and glycomics research has increased considerably in recent years. However, the general development in this field can still be considered as being in its infancy when compared to the genomics and proteomics areas. In terms of bioinformatics in glycobiology, there are several paths of research that are currently in progress. The development of algorithms to reliably support the characterization of glycan structures for high-throughput applications is the most immediate demand of the glycomics community. Additionally, several major glycorelated projects (Consortium for Functional Glycomics [2], KEGG Glycan [3], GLYCOSCIENCES.de [4]) are maturing and provide well-structured glyco-related data that are awaiting data mining and analysis. With the exciting new developments in carbohydrate arrays and automated MS annotation, the analysis of the glycome has reached a new level of sophistication, which requires broader informatics support. This tutorial aims to give an overview of the current status of carbohydrate databases, the newest analytical techniques, as well as the informatics needed for rapid progress in glycomics research.