ParBaum
(Parallelisierung von Maximum Likelihood-Verfahren zur Rekonstruktion eines umfassenden Stammbaums des Lebens aus multiplen Alignments molekularer Daten)
Maximum likelihood based methods are the gold standard for infering phylogeny from molecular sequence data. These methods, however, are highly computing intensive and time consuming, particularly when applied to large sequence datasets. Within the project ParBaum we plan to calculate a comprehensive phylogenetic tree of life from multiple alignments of molecular data applying the maximum likelihood method on parallel computing systems. Therefore, present days algorithms are currently optimized, and new heuristics developed. Applying parallel implementations of these heuristics on high performance computers, like the Hitachi SR8000/F168 at the LRZ-München or the HELICS-Cluster at the IWR-Heidelberg, a significant step towards a maximum likelihood based tree of life will be made.
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REGX II
(Real Environmental Genomix)
The main goal in the BMBF funded project REGX II (Real Environmental Genomics 2) is the functional whole genome analysis 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 our sub-project F the software package ARB is extended by components for reliable management and fast analyses of genome and proteome data. We develop tools for management and concise graphic representation of annotated genome data. Routines are deviced to extract specific data from the genome database in order to accellerate the creation of gene- and protein-alignments. The development of tools for unlimited storage, handling, and analysis of proteome data is one of the major aspects of this project. In expectance of the flood of genome data in the the near future important components for genome database analysis will be distributed or parallelized.
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DNA-Chip
(Entwicklung eines universellen DNA-Chips zum Nachweis von Bakterien in komplexem Probenmaterial)
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 algorithms for designing oligonucleotide probe sets from large sequence databases and implement them to parallel, GUI-based applications. Furthermore tools are deviced for the fast and precise analysis of the complex hybridization profiles resulting from detection experiments with the DNA-chips.
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DB-BIOLOG
(Integrated databases for rRNA and other important gene sequences; parallel programs for automatic search for sequence identifiers )
This project is part of the main research project BIOLOG -- Biodiversity and Global Change 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 culture independant microbial community analyses in various ecosystems.
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