title: The PEDANT genome database.
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.
authors.affiliation: Institute for Bioinformatics, GSF - National Research Center for Environment and Health, Ingolstädter Landstrasse 1, 85764 Neueherberg, Germany. d.frishman@gsf.de
authors.forename: Dmitrij
authors.initials: D
authors.lastname: Frishman
authors.forename: Martin
authors.initials: M
authors.lastname: Mokrejs
authors.forename: Denis
authors.initials: D
authors.lastname: Kosykh
authors.forename: Gabi
authors.initials: G
authors.lastname: Kastenmüller
authors.forename: Grigory
authors.initials: G
authors.lastname: Kolesov
authors.forename: Igor
authors.initials: I
authors.lastname: Zubrzycki
authors.forename: Christian
authors.initials: C
authors.lastname: Gruber
authors.forename: Birgitta
authors.initials: B
authors.lastname: Geier
authors.forename: Andreas
authors.initials: A
authors.lastname: Kaps
authors.forename: Kaj
authors.initials: K
authors.lastname: Albermann
authors.forename: Andreas
authors.initials: A
authors.lastname: Volz
authors.forename: Christian
authors.initials: C
authors.lastname: Wagner
authors.forename: Matthias
authors.initials: M
authors.lastname: Fellenberg
authors.forename: Klaus
authors.initials: K
authors.lastname: Heumann
authors.forename: Hans-Werner
authors.initials: HW
authors.lastname: Mewes
mesh_terms: D000818:Animals; D019295:Computational Biology; D030541:Databases, Genetic; D020440:Gene Duplication; D016678:Genome; D023281:Genomics; D006801:Humans; D016247:Information Storage and Retrieval; D051379:Mice; D025941:Protein Interaction Mapping; D011506:Proteins / Q000737:chemistry / Q000502:physiology; D029701:Saccharomyces cerevisiae Proteins / Q000378:metabolism; D020539:Sequence Analysis, Protein; D017385:Sequence Homology
chemical_list: D011506:Proteins; D029701:Saccharomyces cerevisiae Proteins