The PEDANT genome database

Dmitrij Frishman; Martin Mokrejs; Denis Kosykh; Gabi Kastenmüller; Grigory Kolesov; Igor Zubrzycki; Christian Gruber; Birgitta Geier; Andreas Kaps; Kaj Albermann; Andreas Volz; Christian Wagner; Matthias Fellenberg; Klaus Heumann; Hans Werner Mewes

doi:10.1093/nar/gkg005

The PEDANT genome database

Dmitrij Frishman, Martin Mokrejs, Denis Kosykh, Gabi Kastenmüller, Grigory Kolesov, Igor Zubrzycki, Christian Gruber, Birgitta Geier, Andreas Kaps, Kaj Albermann, Andreas Volz, Christian Wagner, Matthias Fellenberg, Klaus Heumann, Hans Werner Mewes

Life Sciences

Research output: Contribution to journal › Review article › peer-review

102 Scopus citations

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 BioRS™ 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.

Original language	English
Pages (from-to)	207-211
Number of pages	5
Journal	Nucleic Acids Research
Volume	31
Issue number	1
DOIs	https://doi.org/10.1093/nar/gkg005
State	Published - 1 Jan 2003

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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 BioRS{\texttrademark} 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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AU - Zubrzycki, Igor

AU - Gruber, Christian

AU - Geier, Birgitta

AU - Kaps, Andreas

AU - Albermann, Kaj

AU - Volz, Andreas

AU - Wagner, Christian

AU - Fellenberg, Matthias

AU - Heumann, Klaus

AU - Mewes, Hans Werner

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The PEDANT genome database

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