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.
Download full-text PDF |
Source |
|---|---|
| http://www.ncbi.nlm.nih.gov/pmc/articles/PMC165452 | PMC |
| http://dx.doi.org/10.1093/nar/gkg005 | DOI Listing |
Publication Analysis
Top Keywords
Similar Publications
The effect of Fusarium culmorum infection and deoxynivalenol (DON) application on proteome response in barley cultivars Chevron and Pedant.
J Proteomics
October 2017
Laboratory of Plant Stress Biology and Biotechnology, Division of Crop Genetics and Breeding, Crop Research Institute, 161 06 Prague 6 - Ruzyně, Czech Republic.
Fusarium head blight (FHB) disease adversely affects grain quality and final yield in small-grain cereals including barley. In the present study, the effect of an artificial infection with Fusarium culmorum and an application of deoxynivalenol (DON) on barley spikes of cultivars Chevron and Pedant during flowering was investigated at grain mid-dough stage (BBCH 73) 10days after pathogen inoculation (10 dai). Proteomic analysis using a two-dimensional differential gel electrophoresis (2D-DIGE) technique coupled with LC-MS/MS investigated 98 protein spots revealing quantitative or qualitative differences between the experimental variants.
View Article and Find Full Text PDFMIPS: curated databases and comprehensive secondary data resources in 2010.
Nucleic Acids Res
January 2011
Institute for Bioinformatics and Systems Biology, MIPS, Helmholtz Center F Health and Environment, Ingolstädter Landstr 1, D-85764 Neuherberg, Germany.
The Munich Information Center for Protein Sequences (MIPS at the Helmholtz Center for Environmental Health, Neuherberg, Germany) has many years of experience in providing annotated collections of biological data. Selected data sets of high relevance, such as model genomes, are subjected to careful manual curation, while the bulk of high-throughput data is annotated by automatic means. High-quality reference resources developed in the past and still actively maintained include Saccharomyces cerevisiae, Neurospora crassa and Arabidopsis thaliana genome databases as well as several protein interaction data sets (MPACT, MPPI and CORUM).
View Article and Find Full Text PDFPEDANT covers all complete RefSeq genomes.
Nucleic Acids Res
January 2009
Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany.
The PEDANT genome database provides exhaustive annotation of nearly 3000 publicly available eukaryotic, eubacterial, archaeal and viral genomes with more than 4.5 million proteins by a broad set of bioinformatics algorithms. In particular, all completely sequenced genomes from the NCBI's Reference Sequence collection (RefSeq) are covered.
View Article and Find Full Text PDFMIPS: analysis and annotation of genome information in 2007.
Nucleic Acids Res
January 2008
Institute for Bioinformatics (MIPS), German Research Center for Environmental Health, Ingolstaedter Landstrasse 1, D-85764 Neuherberg, Germany.
The Munich Information Center for Protein Sequences (MIPS-GSF, Neuherberg, Germany) combines automatic processing of large amounts of sequences with manual annotation of selected model genomes. Due to the massive growth of the available data, the depth of annotation varies widely between independent databases. Also, the criteria for the transfer of information from known to orthologous sequences are diverse.
View Article and Find Full Text PDFApplying negative rule mining to improve genome annotation.
BMC Bioinformatics
July 2007
Institute for Bioinformatics, GSF-National Research Center for Environment and Health, Neuherberg, Germany.
Background: Unsupervised annotation of proteins by software pipelines suffers from very high error rates. Spurious functional assignments are usually caused by unwarranted homology-based transfer of information from existing database entries to the new target sequences. We have previously demonstrated that data mining in large sequence annotation databanks can help identify annotation items that are strongly associated with each other, and that exceptions from strong positive association rules often point to potential annotation errors.
View Article and Find Full Text PDFWant AI Summaries of new PubMed Abstracts delivered to your In-box?
Enter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!