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PMID: 12519983 Published · ppublish English Journal Article

The PEDANT genome database.

Nucleic acids research ·Vol. 31 ·No. 1 ·2003-01-01 ·Pages 207-11

Frishman D, Mokrejs M, Kosykh D, Kastenmüller G, Kolesov G, Zubrzycki I, Gruber C, Geier B, Kaps A, Albermann K, Volz A, Wagner C, Fellenberg M, Heumann K, Mewes HW

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.

MeSH Terms
Animals Computational Biology Databases, Genetic Gene Duplication Genome Genomics Humans Information Storage and Retrieval Mice Protein Interaction Mapping Proteins/chemistry,physiology Saccharomyces cerevisiae Proteins/metabolism Sequence Analysis, Protein Sequence Homology
Chemicals
Proteins Saccharomyces cerevisiae Proteins
Authors & Affiliations
15 authors, click to expand affiliations / ORCID
Frishman Dmitrij
Institute for Bioinformatics, GSF - National Research Center for Environment and Health, Ingolstädter Landstrasse 1, 85764 Neueherberg, Germany. [email protected]
Mokrejs Martin
Kosykh Denis
Kastenmüller Gabi
Kolesov Grigory
Zubrzycki Igor
Gruber Christian
Geier Birgitta
Kaps Andreas
Albermann Kaj
Volz Andreas
Wagner Christian
Fellenberg Matthias
Heumann Klaus
Mewes Hans-Werner
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Article Info
Journal
Nucleic acids research
Abbr.
Nucleic Acids Res
ISSN
1362-4962
DOI
10.1093/nar/gkg005
Email
[email protected]
Published
2003-01-01
Pages
207-11
Language
English
Region
England
NLM ID
0411011
PMCID
PMC165452
Subset
IM
External Links
PubMed source DOI: 10.1093/nar/gkg005 PMC Full Text View journal details
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