Bioinformatics for glycomics: status, methods, requirements and perspectives.
The term 'glycomics' describes the scientific attempt to identify and study all the glycan molecules - the glycome - synthesised by an organism. The aim is to create a cell-by-cell catalogue of glycosyltransferase expression and detected glycan structures. The current status of databases and bioinformatics tools, which are still in their infancy, is reviewed. The structures of glycans as secondary gene products cannot be easily predicted from the DNA sequence. Glycan sequences cannot be described by a simple linear one-letter code as each pair of monosaccharides can be linked in several ways and branched structures can be formed. Few of the bioinformatics algorithms developed for genomics/proteomics can be directly adapted for glycomics. The development of algorithms, which allow a rapid, automatic interpretation of mass spectra to identify glycan structures is currently the most active field of research. The lack of generally accepted ways to normalise glycan structures and exchange glycan formats hampers an efficient cross-linking and the automatic exchange of distributed data. The upcoming glycomics should accept that unrestricted dissemination of scientific data accelerates scientific findings and initiates a number of new initiatives to explore the data.
von der Lieth
Claus-Wilhelm
CW
German Cancer Research Center, Central Spectroscopic Department B090, Im Neuenheimer Feld 280, D-69120 Heidelberg, Germany. w.vonderlieth@dkfz.de
Bohne-Lang
Andreas
A
Lohmann
Klaus Karl
KK
Frank
Martin
M
D000818:Animals; D002236:Carbohydrate Conformation; D019295:Computational Biology / Q000379:methods; D016208:Databases, Factual; D006031:Glycosylation; D016695:Glycosyltransferases / Q000378:metabolism; D013058:Mass Spectrometry; D008958:Models, Molecular; D011134:Polysaccharides / Q000737:chemistry / Q000378:metabolism; D020543:Proteome; D012984:Software
D011134:Polysaccharides; D020543:Proteome; D016695:Glycosyltransferases