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PEDANT


NAR Molecular Biology Database Collection entry number 354
Frishman, D.1, Mokrejs, M.1, Kosykh, D.1, Kastenmüller, G.1, Kolesov, G.1, Zubrzycki, I.1, Gruber, C.2, Geier, B.2, Kaps, A.2, Albermann, K.2, Volz, A.2, Wagner, C.2, Fellenberg, M.2, Heumann, K.2, Mewes, H.-W.3
1Institute for Bioinformatics, GSF - National Research Center for Environment and Heath, Ingolstädter Landstraße 1, 85764 Neueherberg, Germany
2Biomax Informatics AG, Lochhamer Straße 11, 82152 Martinsried, Germany
3Department of Genome-oriented Bioinformatics, Wissenschaftszentrum Weihenstephan, Technische Universität München, 85350 Freising, German

Database Description

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. Nearly 3000 completely sequenced publicly available eukaryotic, eubacterial, archaeal and viral genomes with more than 4.5 million proteins have been processed so far.
In particular, all completely sequenced genomes from the NCBI's Reference Sequence collection (RefSeq) (1) are covered. The PEDANT processing pipeline has been sped up by an order of magnitude through the utilization of precalculated similarity information stored in the similarity matrix of proteins (SIMAP) database (2), making it possible to process newly sequenced genomes immediately as they become available.
For programmatic access Web Services are available at http://pedant.gsf.de/webservices.jsp.

References

1. Pruitt, K.D., Tatusova, T. and Maglott, D.R. (2007) NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Res., 35, D61-D65.
2. Rattei, T., Tischler, P., Arnold, R., Hamberger, F., Krebs, J., 40 Krumsiek, J., Wachinger, B., Stümpflen, V. and Mewes, H.-W. (2008) SIMAP - structuring the network of protein similarities. Nucleic Acids Res., 36, D289-D292.


Go to the abstract in the NAR 2009 Database Issue.
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