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Nucleic Acids Research, 2003, Vol. 31, No. 1 207-211
© 2003 Oxford University Press

The PEDANT genome database

Dmitrij Frishman*,1, Martin Mokrejs1, Denis Kosykh1, Gabi Kastenmüller1, Grigory Kolesov1, Igor Zubrzycki1, Christian Gruber2, Birgitta Geier2, Andreas Kaps2, Kaj Albermann2, Andreas Volz2, Christian Wagner2, Matthias Fellenberg2, Klaus Heumann2 and Hans-Werner Mewes1,3

1 Institute for Bioinformatics, GSF - National Research Center for Environment and Health, Ingolstädter Landstraße 1, 85764 Neueherberg, Germany 2 Biomax Informatics AG, Lochhamer Straße 11, 82152 Martinsried, Germany 3 Department of Genome-oriented Bioinformatics, Wissenschaftszentrum Weihenstephan, Technische Universität München, 85350 Freising, Germany

*To whom correspondence should be addressed. Tel: +49 89 31874201; Fax: +49 89 31873585; Email: d.frishman{at}gsf.de

ABSTRACT

The PEDANT genome database (http://pedant.gsf.de) provides exhaustive automatic analysis of genomic sequences by a large variety of established bioinformatics tools through a comprehensive Web-based user interface. One hundred and seventy seven completely sequenced and unfinished genomes have been processed so far, including large eukaryotic genomes (mouse, human) published recently. In this contribution, we describe the current status of the PEDANT database and novel analytical features added to the PEDANT server in 2002. Those include: (i) integration with the BioRSTM data retrieval system which allows fast text queries, (ii) pre-computed sequence clusters in each complete genome, (iii) a comprehensive set of tools for genome comparison, including genome comparison tables and protein function prediction based on genomic context, and (iv) computation and visualization of protein–protein interaction (PPI) networks based on experimental data. The availability of functional and structural predictions for 650 000 genomic proteins in well organized form makes PEDANT a useful resource for both functional and structural genomics.


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