Ernst Kretschmann

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MOTIVATION The gap between the amount of newly submitted protein data and reliable functional annotation in public databases is growing. Traditional manual annotation by literature curation and sequence analysis tools without the use of automated annotation systems is not able to keep up with the ever increasing quantity of data that is submitted. Automated(More)
Analyses of 55 individual and 31 concatenated protein data sets encoded in Reclinomonas americana and Marchantia polymorpha mitochondrial genomes revealed that current methods for constructing phylogenetic trees are insufficiently sensitive (or artifact-insensitive) to ascertain the sister of mitochondria among the current sample of eight(More)
Analyses of 55 individual and 31 concatenated protein data sets encoded in Reclinomonas americana and Marchantia polymorpha mitochondrial genomes revealed that current methods for constructing phylogenetic trees are insufficiently sensitive (or artifact-insensitive) to ascertain the sister of mitochondria among the current sample of eight aproteobacterial(More)
SUMMARY The CluSTr database employs a fully automatic single-linkage hierarchical clustering method based on a similarity matrix. In order to compute the matrix, first all-against-all pair-wise comparisons between protein sequences are computed using the Smith-Waterman algorithm. The statistical significance of the similarity scores is then assessed using a(More)
Programmatic access to the UniProt Knowledgebase (UniProtKB) is essential for many bioinformatics applications dealing with protein data. We have created a Java library named UniProtJAPI, which facilitates the integration of UniProt data into Java-based software applications. The library supports queries and similarity searches that return UniProtKB entries(More)
1 Institute of Botany III, University of Düsseldorf, 40225 Düsseldorf, Germany 2 European Bioinformatics Institute, Hinxton, Cambridge, CB10 1SD, United Kingdom 3 Max-Planck Institut für Züchtungsforschung, Carl von Linné-Weg 10, 50829 Köln, Germany 4 McGill Centre for Bioinformatics, 3775 University St., Montréal, Québec, H3A 2B4, Canada 5 Department of(More)
In this study, we present two freely available and complementary Distributed Annotation System (DAS) resources: a DAS reference server that provides up-to-date sequence and annotation from UniProt, with additional feature links and database cross-references from InterPro and a DAS client implemented using Java and Macromedia Flash that is optimized for the(More)
A novel way to represent knowledge using extended semantic networks as underlying model is presented. This approach extends the semantic network idea from its frequent application in presenting human-readable data correlations into a basis for a general computerized data modelling technology. The method was successfully applied using biological data from(More)