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RUNNING PROJECTS

  • Whole Genome Sequencing Of Environmentally Relevant Bacteria (BMBF-03F0279F)

    The aims in the BMBF funded project REGX -- Real Environmental Genomics is sequencing and analyses of whole genomes of three important bacteria from marine sediments (Pirellula sp. strain 1, Desulfobacterium autotrophicum strain HRM2, and Desulfotalea psychrophila strain LSv54). Gen expression will be studied under different physiological conditions. In sub-project F the software package ARB will be extended by components for reliable management and fast analyses of genome and expression data. We intend to develop tools for management and concise graphic presentation of annotated genome data. Routines will be deviced to extract gene data from the genome database and create gene- and protein-alignments. In expectance of the flood of genome data in a few years the routines for genome analysis database management will be parallelized.

  • Universal Chip for Microorganisms (Bayerische Forschungsstiftung)

    Cooperation between LRR-TUM, LS Mikrobiologie, TUM, and MWG-Biotech AG. We intend to develop DNA-Chips (microarrays) equipped with rRNA-targeted, as well as functional gene-targeted oligonucleotide probes for rapid and comprehensive identification of microorganisms in environmental samples. The project comprises design and production of the DNA-Chips, as well as experimental optimization of DNA-Chip based detection of microorganisms in in complex samples. We are developing software for complete automation of chip design, update and evaluation of the chips according to their probe equipment. Furthermore tools will be deviced for fast and precise analysis of the complex hybridization profiles resulting from detection experiments with the DNA-chips.

  • Automatic Generation And Maintenance Of Integrated Databases For rRNA And Other Important Gene Sequences; Development, Optimization, And Parallelization Of Software For Automatic Search For Sequence Identifiers In Terms Of Diversity Analyses (BMBF 01LC9902)

    This project is part of the main research project BIOLOG -- Biodiversität und Globaler Wandel of the BMBF. Our aim is to generate, optimize and update sequence- and probe-databases for genes and organisms, important for dbiodiversity analyses.Therefore, softwaretools of the ARB-software package are upgraded or newly developed. Tools for automatic updating of the rRNA alignments are centered, as well as components for automatic retrieval of Sequence identifiers for large groups of organisms. Thereby, probe sets are designed fully automatically, for ultra rapid determination of organismal composition of ecosystems.

  • ParBaum (KONWIHR)

    Within ParBaum comprehensive phylogenetic trees of life will be calculated from multiple alignments of molecular data applying the maximum likelihood method on one of Germans fastest supercomputer, the Hitachi SR8000/F168. Therefore, algorithms based on the maximum likelihood will be developed, optimized, parallelized, and applied on different parallel computers (i.e. the Hitachi SR8000/F168) as well as on computer clusters. One of the major results of ParBaum is RAxML, the currently fastest program for calculating phylogenetic trees from nucleic acid sequence alignments based on the maximum likelihood criteria.

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Harald Meier
Last modified: Tue Jan 23 17:31:39 CEST 2008