Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2005 Jan 1;33(Database issue):D308-10.
doi: 10.1093/nar/gki019.

The PEDANT genome database in 2005

M Louise Riley  1 , Thorsten Schmidt, Christian Wagner, Hans-Werner Mewes, Dmitrij Frishman
Affiliations

The PEDANT genome database in 2005

M Louise Riley et al. Nucleic Acids Res. .

Abstract

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.

PubMed Disclaimer

Figures

Figure 1
Figure 1
Growth of the number of annotated genomes in the PEDANT database since 1998. *Number as of September 1, 2004.
Figure 2
Figure 2
Number of annotated genomes (A) and protein sequences (B) in different genome categories.
Figure 3
Figure 3
An illustration of the functional and structural content of the PEDANT database. The figure shows the percentage of protein sequences associated with PFAM sequence motifs, SCOP structural domains and MIPS functional categories, as well as any combinations of these three attributes.
Figure 4
Figure 4
The FunCat distribution of all 334 genomes in PEDANT. Here, the relative amounts of proteins that are assigned to one or more of six general FunCat classes are shown. Since proteins can be assigned to more than one functional category, the total fraction exceeds 100%.
See this image and copyright information in PMC

References

    1. Frishman D. and Mewes,H.W. (1997) PEDANTic genome analysis. Trends Genet., 13, 415–416.
    1. Boeckmann B., Bairoch,A., Apweiler,R., Blatter,M.C., Estreicher,A., Gasteiger,E., Martin,M.J., Michoud,K., O'Donovan,C., Phan,I. et al. (2003) The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003. Nucleic Acids Res., 31, 365–370. - PMC - PubMed
    1. Wu C.H., Nikolskaya,A., Huang,H., Yeh,L.S., Natale,D.A., Vinayaka,C.R., Hu,Z.Z., Mazumder,R., Kumar,S., Kourtesis,P. et al. (2004) PIRSF: family classification system at the Protein Information Resource. Nucleic Acids Res., 32, D112–D114. - PMC - PubMed
    1. Frishman D., Mokrejs,M., Kosykh,D., Kastenmuller,G., Kolesov,G., Zubrzycki,I., Gruber,C., Geier,B., Kaps,A., Albermann,K. et al. (2003) The PEDANT genome database. Nucleic Acids Res., 31, 207–211. - PMC - PubMed
    1. Tatusov R.L., Fedorova,N.D., Jackson,J.D., Jacobs,A.R., Kiryutin,B., Koonin,E.V., Krylov,D.M., Mazumder,R., Mekhedov,S.L., Nikolskaya,A.N., et al. (2003) The COG database: an updated version includes eukaryotes. BMC Bioinformatics, 4, 41–54. - PMC - PubMed