The PEDANT genome database in 2005

The PEDANT genome database (http://pedant.gsf.de) contains pre-computed bioinformatics analyses of publicly available genomes. Its main mission is to provide robust automatic annotation of the vast majority of amino acid sequences, which have not been subjected to in-depth manual curation by human experts in high-quality protein sequence databases. By design PEDANT annotation is genome-oriented, making it possible to explore genomic context of gene products, and evaluate functional and structural content of genomes using a category-based query mechanism. At present, the PEDANT database contains exhaustive annotation of over 1 240 000 proteins from 270 eubacterial, 23 archeal and 41 eukaryotic genomes.

[1]  Dmitrij Frishman,et al.  Illuminating the Evolutionary History of Chlamydiae , 2004, Science.

[2]  Dmitrij Frishman,et al.  The PEDANT genome database , 2003, Nucleic Acids Res..

[3]  Maria Jesus Martin,et al.  The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003 , 2003, Nucleic Acids Res..

[4]  Philip E. Bourne,et al.  The distribution and query systems of the RCSB Protein Data Bank , 2004, Nucleic Acids Res..

[5]  H. Mewes,et al.  Overview of the yeast genome. , 1997, Nature.

[6]  Dmitrij Frishman,et al.  MIPS: a database for genomes and protein sequences , 1999, Nucleic Acids Res..

[7]  Darren A. Natale,et al.  The COG database: an updated version includes eukaryotes , 2003, BMC Bioinformatics.

[8]  Dmitrij Frishman,et al.  PEDANTic genome analysis , 1997 .

[9]  H. Mewes,et al.  The FunCat, a functional annotation scheme for systematic classification of proteins from whole genomes. , 2004, Nucleic acids research.

[10]  Dmitrij Frishman,et al.  The genome sequence of the thermoacidophilic scavenger Thermoplasma acidophilum , 2000, Nature.

[11]  Robert S. Ledley,et al.  PIRSF: family classification system at the Protein Information Resource , 2004, Nucleic Acids Res..

[12]  Tim J. P. Hubbard,et al.  SCOP database in 2004: refinements integrate structure and sequence family data , 2004, Nucleic Acids Res..

[13]  E. Mauceli,et al.  The genome sequence of the filamentous fungus Neurospora crassa , 2003, Nature.

[14]  The Arabidopsis Genome Initiative.  Analysis of the genome sequence of the flowering plant Arabidopsis thaliana , 2000, Nature.