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Glycobiology Advance Access originally published online on September 16, 2009
Glycobiology 2009 19(12):1563-1567; doi:10.1093/glycob/cwp137
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© The Author 2009. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oxfordjournals.org

Glycome-DB.org: A portal for querying across the digital world of carbohydrate sequences

René Ranzinger1,2, Martin Frank2, Claus-Wilhelm von der Lieth2 and Stephan Herget2

2 German Cancer Research Center, Molecular Structure Analysis (W160), Molecular Modeling Group, Im Neuenheimer Feld 280, D-69120 Heidelberg, Germany

1 To whom correspondence should be addressed: e-mail: rene.ranzinger{at}glycome-db.org

Received on April 29, 2009; revised on ; accepted on August 31, 2009

Despite ongoing harmonization efforts, the major carbohydrate sequence databases following the first initiative in this field, CarbBank, are still isolated islands, with mechanisms for automatic structure exchange and comparison largely missing. This unfavorable situation has been overcome with a systematic data integration effort, resulting in the GlycomeDB, a meta-database for public carbohydrate sequences. It contains at present 35,056 unique structures in GlycoCT encoding, referencing more than 100,000 external records from 1845 different taxonomic sources. We have created a user-friendly, web-based graphical interface which allows taxonomic and structural data to be entered and searched for. The structural search possibilities include substructure search, similarity search, and maximum common substructure. A novel search refinement mechanism allows the assembly of complex queries. With GlycomeDB (www.glycome-db.org), it is now possible to use a single portal to access all digitally encoded, public structural data in glycomics and to perform complex queries with the help of a web-based user interface.

Key words: carbohydrate sequence database / data warehouse / glycomics / search engine / web portal


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