Biomedical subjects

Werner Mewes

Publications and source records attributed to Werner Mewes.

3 recordsLinked to original sources

PubMed2005

SIMAP--the similarity matrix of proteins.

MOTIVATION: Sequence similarity searches are of great importance in bioinformatics. Exhaustive searches for homologous proteins in databases are computationally expensive and can be replaced by a database of pre-calculated homologies in many cases. Retrieving similarities from an incrementally updated database instead of repeatedly recalculating them should provide homologs much faster and frees computational resources for other purposes. RESULTS: We have implemented SIMAP-a database containing the similarity space formed by almost all amino acid sequences from public databases and completely sequenced genomes. The database is capable of handling very large datasets and allows incremental updates. We have implemented a powerful backbone for similarity computation, which is based on FASTA heuristics. By providing WWW interfaces as well as web services, we make our data accessible to the worldwide community. We have also adapted procedures to detect putative orthologs as example applications. AVAILABILITY: The SIMAP portal page providing links to SIMAP services is publicly available: http://mips.gsf.de/services/analysis/simap/. The web services can be accessed under http://mips.gsf.de/proj/hobitws/services/RPCSimapService?wsdl and http://mips.gsf.de/proj/hobitws/services/DocSimapService?wsdl

Algorithms↗

PubMed2005

PRIME: a graphical interface for integrating genomic/proteomic databases.

Data mining, finding and integration of information about proteins of interest, is an essential component in modern biological and biomedical research. Even when focusing on a single organism and only on a small number of proteins, there are often dozens fo data sources containing relevant information. We are developing PRIME, a protein information environment, to serve as a virtual central database which integrates distributed heterogeneous information about proteins (linked by common identifier). PRIME has powerful capabilities to visualize all kinds of protein annotation in specialized views. These views can be displayed side by side at the same time and can be synchronized in order to show simultaneously different aspects of identical proteins. These features allow a quick and comprehensive overview of properties of single proteins or protein sets.

Computational Biology↗

PubMed2003

The genome sequence of the filamentous fungus Neurospora crassa.

Neurospora crassa is a central organism in the history of twentieth-century genetics, biochemistry and molecular biology. Here, we report a high-quality draft sequence of the N. crassa genome. The approximately 40-megabase genome encodes about 10,000 protein-coding genes--more than twice as many as in the fission yeast Schizosaccharomyces pombe and only about 25% fewer than in the fruitfly Drosophila melanogaster. Analysis of the gene set yields insights into unexpected aspects of Neurospora biology including the identification of genes potentially associated with red light photobiology, genes implicated in secondary metabolism, and important differences in Ca2+ signalling as compared with plants and animals. Neurospora possesses the widest array of genome defence mechanisms known for any eukaryotic organism, including a process unique to fungi called repeat-induced point mutation (RIP). Genome analysis suggests that RIP has had a profound impact on genome evolution, greatly slowing the creation of new genes through genomic duplication and resulting in a genome with an unusually low proportion of closely related genes.

Calcium Signaling↗