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Welcome to the PEDANT 3 database - a Protein Extraction, Description and ANalysis Tool

The pedant genome database provides exhaustive automatic analysis of genomic sequences by a large variety of bioinformatics tools. For example the following pre-computed analyses are available to analyse protein function: Blast similarity searches against the non-redundant protein sequence database, motif searches against the Pfam, BLOCKS and PROSITE databases. Prediction of cellular roles and functions are made based on high stringency BLAST searches against protein sequences with manually assigned functional categories according to the Functional Catalogue (FunCat) developed by MIPS and Biomax AG.

Protein structure analysis includes the similarity-based identification of known 3D structures and structural domains, by searching against the PDB and SCOP databases, and predictions of transmembrane regions, low similarity regions and non-globular domains.

References: Walter et al. 2009Riley et al. 20072005Frishman et al. 200320011997

News

2013-09-15A new release of PEDANT is ready to use. It is based on RefSeq v60 and InterPro v43.
2013-03-01PEDANT is online again. We started to reimport the RefSeq genomes (about 5-10 per week for the moment) and make them available again.
2012-07-16Due to a hardware crash of our storage system, we switched PEDANT into maintenance mode. Therefore, only a limited set of genomes is currently available.
2009-07-01The PEDANT web service URL has changed to http://pedant.helmholtz-muenchen.de.de/webservice.
2008-10-21A new PEDANT paper was published in Nucleic Acids Research (see references).
2008-09-01All viral genomes available at RefSeq were imported.
2008-04-02Fixed long-standing problem with gene coordinates, shifted by one (+1). All microbial genomes were affected.
Recalculation of FunCat 2.1 is currently running.
New webservice is available.
2008-03-26New eukaryotic genomes have been added as well as the taxonomic selection for metazoa.
Now, the main page shows only the recently computed genomes of the last three months.

Genomes analysed by PEDANT

Show recently imported genomes starting with the letter:

[A] [B] [C] [D] [E] [F] [G] [H] [I] [J] [K] [L] [M] [N] [O] [P] [Q] [R] [S] [T] [U] [V] [W] [X] [Y] [Z]

Abbreviations:  B - Genome Browser;  G - Gold Metadata;  P - NCBI BioProject;  T - NCBI Taxonomy U - UniProtKB SQLException: com.mysql.jdbc.exceptions.jdbc4.MySQLNonTransientConnectionException: Could not create connection to database server. Attempted reconnect 3 times. Giving up.
Organism NameBGPTU