Projects in Computational Biology

Overview

The MPCDF hosts various bioinformatics services for MPG-internal and public use, offers application support for bioinformatics projects of the Max-Planck-Society, contributes original software development and participates in various research projects.

 

Technical Documentation

 

Scientific Applications

Genome annotation projects

With the help of the MIGenAS infrastructure, a number of microbial genomes, among them some highly relevant model organisms, were “finished” and published (see below for references), several other projects are currently in progress. Key components which are employed here comprise the Phred/Phrap assembler package (ported by MPCDF to 64-bit Linux and parallelized for running on large shared-memory systems), GenDB (MPCDF installation of GenDB 2.0, 2.2), the MIGenAS web toolkit, HaloLex, and relevant sequence and annotation databases.

Metagenomics

One of the highlights in this area was the analysis of ancient DNA from a Siberian Mammoth fossil, for which considerable parts of the computational analysis were conducted with the MIGenAS infrastructure.

Other applications

Many projects and working groups are taking advantage of dedicated support in the form of general and bioinformatics-specific user support and application consulting, hardware resources, etc.


Hosting, housing and consulting

MPCDF provides consulting to several bioinformatics-related projects and houses and hosts hardware and various web applications, e.g.
  • Galaxy (https://www.bioinfo.mpg.de/galaxy): Galaxy is an open source, web-based platform for data intensive biomedical research. The MPCDF is operating a Galaxy instance for the MPG, in collaboration with several Max Planck Institutes.
  • Movebank (http://www.movebank.org): a free, online database of animal tracking data (developed at MPI for Ornithology and collaborators)
  • MIGenAS toolkit (2005- 2017)  web-based toolkit and workflow engine for integrated sequence analysis (developed at MPCDF):
  • HaloLex (https://www.halolex.mpg.de): comprehensive annotation and information system for prokaryotic genome and proteome data (developed at MPI of Biochemistry and MPCDF) access restricted/on request

 

Selected Publications

  • BioEM: GPU-accelerated computing of Bayesian inference of electron microscopy images. P. Cossio, D. Rohr, F. Baruffa, M. Rampp, V. Lindenstruth, G. Hummer. to appear in Computer Physics Communications (2016) (arXiv:1609.06634)
  • Dnmt2-dependent methylomes lack defined DNA methylation patterns. G. Raddatz, P. M. Guzzardo, N. Olova, M. R. Fantappié, M. Rampp, M. Schaefer, W. Reik, G. J. Hannon, F. Lyko PNAS (2013). doi:10.1073/pnas.1306723110
  • Genome of the Haloarchaeon Natronomonas moolapensis, a Neutrophilic Member of a Previously Haloalkaliphilic Genus. Dyall-Smith M.L., Pfeiffer F., Oberwinkler T., Klee K., Rampp M., Palm P., Gross K., Schuster S.C., Oesterhelt D. Genome Announc. (2013). doi: 10.1128/genomeA.00095-13
  • Chloride & organic osmolytes: a hybrid strategy to cope with elevated salinities by the moderately halophilic, chloride-dependent bacterium Halobacillus halophilus. Saum S., Pfeiffer F., Palm P., Rampp M., Schuster S., Müller V., Oesterhelt D., Environmental Microbiology (2012). doi: 10.1111/j.1462-2920.2012.02770.x
  • The complete genome sequence of Thermoproteus tenax: A physiologically versatile member of the Crenarchaeota. Siebers B., Raddatz G., Zaparty M., Tjaden B., Albers S.V., Bell S.D., Blombach F., Kletzin A., Kyrpides N., Lanz C., Plagens A., Rampp M., Rosinus A., von Jan M., Makarova K., Klenk H.P., Schuster S.C., Hensel R. PLoS ONE 6(10): e24222 (2011). doi:10.1371/journal.pone.0024222.
  • Haloquadratum walsbyi: Limited Diversity in a Global Pond. Dyall-Smith, M.L., F. Pfeiffer, K. Klee, P. Palm, K. Gross, S.C. Schuster, M. Rampp, D. Oesterhelt PLoS ONE 6(6): e20968 (2011) doi:10.1371/journal.pone.0020968
  • A blueprint of ectoine metabolism from the genome of the industrial producer Halomonas elongata DSM 2581T. Schwibbert, K., A. Marin Sanguino, I. Bagyan, G. Heidrich, G. Lentzen, H. Seitz, M. Rampp, S.C. Schuster, H.-P. Klenk, F. Pfeiffer, D. Oesterhelt, H.J. Kunte. Environmental Biology (2010)
  • Pfeiffer, F., A. Broicher, Th. Gillich, K. Klee, J. Mejia, M. Rampp, D. Oesterhelt
    Genome information management and integrated data analysis with HaloLex. Archives of Microbiology 190(3), 281-299 (2008)
  • Rampp, M., T. Soddemann, H. Lederer:
    The MIGenAS integrated bioinformatics toolkit for web-based sequence analysis. Nucleic Acids Research 34 (Web Server issue), W15-W19 (2006).
  • Bolhuis H, Palm P, Wende A, Falb M, Rampp M, Rodriguez-Valera F, Pfeiffer F, Oesterhelt D.:
    The genome of the square archaeon Haloquadratum walsbyi: life at the limits of water activity. BMC Genomics, 7 169 (2006)
  • Poinar,H., C. Schwarz, J. Qi, B. Shapiro, R. MacPhee, B. Buigues, A. Tikhonov, D. Huson, L. Tomosho, A. Auch, M. Rampp, W. Miller and S. Schuster:
    Metagenomics to paleogenomics: Large scale sequencing of Mammoth DNA. Science 311, 5759, 392-394 (2006).
  • Rampp,M., T. Soddemann:
    A Work Flow Engine for Microbial Genome Research. In "Forschung und wissenschaftliches Rechnen 2004", K.Kremer, V.Macho (eds.), GWDG Report 68, 23-46 (2005).
  • Baar,C., M. Eppinger, G. Raddatz, J. Simon, C. Lanz, O. Klimmek, R. Nandakumar, R. Gross, A. Rosinus, H. Keller, P. Jagtap, B. Linke, F. Meyer, H. Lederer and S. Schuster:
    Complete genome sequence and analysis of Wolinella succinogenes. PNAS 100, 20, 11690-11695 (2003).
  • Falb,M., Pfeiffer,F., Palm,P., Rodewald,K., Hickmann,V.,Tittor,J. and Oesterhelt,D.: Living with two extremes: Conclusions from the genome sequence of Natronomonas pharaonis. Genome Res. (2005) 15(10):1336-43
  • Bolhuis H, Palm P, Wende A, Falb M, Rampp M, Rodriguez-Valera F, Pfeiffer F, Oesterhelt D.: The genome of the square archaeon Haloquadratum walsbyi: life at the limits of water activity. BMC Genomics, 7 169 (2006)
  • Pfeiffer F, Schuster SC, Broicher A, Falb M, Palm P, Rodewald K, Ruepp A, Soppa J, Tittor J, Oesterhelt D.: Evolution in the laboratory: the genome of Halobacterium salinarum strain R1 compared to that of strain NRC-1. Genomics. 2008 Jun;91(6):548-52
  • Eppinger, M., Baar C, Linz B, Raddatz G, Lanz C, Keller H, Morelli G, Gressmann H, Achtman M, Schuster SC: Who ate whom? Adaptive Helicobacter genomic changes that accompanied a host jump from early humans to large felines. PLOS Genetics, 2(7), e120 (2006)
  • Saenz, H.L., P. Engel, M.C. Stoeckli, C. Lanz, G. Raddatz, M. Vayssier-Taussat, R. Birtles, S.C. Schuster, C. Dehio: Genomic analysis of Bartonella identifies type IV secretion systems as host adaptability factors, Nature Genetics, 39(12):1469-76 (2007)
  • Zimmerer, H.: Evaluation of sequence comparison methods for metagenomics. Diplomarbeit, Eberhard Karls Universität Tübingen, (2007)
  • Meyer F, Goesmann A, McHardy AC, Bartels D, Bekel T, Clausen J, Kalinowski J, Linke B, Rupp O, Giegerich R, Pühler A.: GenDB--an open source Genome annotation system for prokaryote genomes. Nucleic Acids Res. 2003 Apr 15;31(8):2187-95

 

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