D354–D357 Nucleic Acids Research, 2007, Vol. 35, Database issue doi:10.1093/nar/gkl1005 Published online 5 December 2006 PEDANT genome database: 10 years online M. Louise Riley 1 , Thorsten Schmidt2, Irena I. Artamonova 1 , Christian Wagner3, Andreas Volz3, Klaus Heumann 3 , Hans-Werner Mewes1,2 and Dmitrij Frishman1,2,* 1Institute for Bioinformatics, GSF-National Research Center for Health and Environment, Ingolsta¨ dter Landstrasse 1, 85764 Neuherberg, Germany, 2Department of Genome-oriented Bioinformatics, Wissenschaftszentrum Weihenstephan, Technische Universita¨ t Mu¨ nchen, 85350 Freising, Germany and 3Biomax Informatics AG, Lochhamer Strasse 9, 82152 Martinsried, Germany Received September 15, 2006; Accepted October 30, 2006 ABSTRACT The PEDANT genome database provides exhaustive annotation of 468 genomes by a broad set of bio- informatics algorithms. We describe recent devel- opments of the PEDANT Web server. The all-new Graphical User Interface (GUI) implemented in JavaTM allows for more efficient navigation of the genome data, extended search capabilities, user customization and export facilities. The DNA and Protein viewers have been made highly dynamic and customizable. We also provide Web Services to access the entire body of PEDANT data program- matically. Finally, we report on the application of association rule mining for automatic detection of potential annotation errors. PEDANT is freely acces- sible to academic users at http://pedant.gsf.de. INTRODUCTION The PEDANT genome database was ﬁrst announced in a short note entitled ‘PEDANTic genome analysis’ which appeared in Trends in Genetics in 1997 (1) and reported computational analysis of seven completely sequenced and two partial genomes available at that time. From the very beginning the main mission of PEDANT was deﬁned as ﬁll- ing the gap between manually curated high quality protein sequence databases, such as UniProt/Swiss-Prot (2), and the enormous amounts of other protein sequences produced by genome sequencing projects at an ever increasing pace. Over the past decade the PEDANT genome database was pro- duced by systematically applying an automatic annotation pipeline to genome data released in the public domain. These efforts resulted in one of the most comprehensive cur- rently available genome databases which includes 468 organ- isms from all three domains of life. More than 1.76 million proteins sequences have been annotated. The PEDANT software suite has been described in detail elsewhere (3). Here we report on three new features of the PEDANT Web server: (i) an all-new graphical user interface (GUI), (ii) availability of Web Services and (iii) rule-based detection of annotation errors. New Graphical User Interface (GUI) The current version of the PEDANT software familiar to most users was introduced several years ago and is known as version 2 (3). In 2006 we were deploying and testing the all-new version 3 which represents a complete re-implementation of the PEDANT software in the Java programing language. PEDANT3 is a platform-independent client–server application for enterprise-scale molecular sequence analysis with advanced features such as highly dynamic workﬂow-based process management, direct inter- face to computing grids, support for essentially all existing SQL database management systems, open architecture for easy integration of additional algorithms, and powerful script- ing interfaces (D. Frishman et al., manuscript in preparation). Migration of PEDANT genomes to the new version 3 is currently in progress and will be accomplished by mid- 2007. So far we have completed a pilot study to annotate 40 genomes to demonstrate the advantages of PEDANT3. The new version of the PEDANT GUI can be viewed by selecting any genome with a ‘new’ icon next to it on the PEDANT home page. The PEDANT GUI has been made user-conﬁgurable and supports four main types of windows: (i) sequence analysis: information about the complete analysis with links to ORF lists of the individual algorithms, (ii) gene report: information about a selected gene, (iii) contig report: information about a selected contig and (iv) genetic element report (where avail- able): information about a selected nonprotein coding genetic element. On selection of a PEDANT3 genome, the analysis window is opened displaying a list of genes and their best- blast hits. The left-hand panel contains a context-dependent navigation tree that makes available different choices depen- dent on the particular view the user is working with. A report page can be displayed for each gene by selecting its code. The report page (Figure 1) is split into different sec- tions (Overview, Protein function, Protein structure, Protein *To whom correspondence should be addressed. Tel: +49 8161 712134; Fax: +49 8161 712186; Email: d.frishman@wzw.tum.de 2006 The Author(s). This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/ by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.