Seminars of the Focus Area Complex Systems

Prof. Dr. C. Beta, Prof. Dr. K. Dethloff, Prof. Dr. R. Engbert, Prof. Dr. M. Holschneider, Prof. Dr. W. Huisinga, Prof. Dr. Ralf Metzler, Prof. Dr. A. Pikovsky, Prof. Dr. S. Reich, Prof. Dr. M. Rosenblum, Prof. Dr. G. Rüdiger, Prof. Dr. T. Scheffer, Prof. Dr. F. Scherbaum, Prof. Dr. J. Selbig, Prof. Dr. F. Spahn

Seminar

Speaker: Sebastian Proost, Department of Plant Systems Biology, VIB, Ghent, Belgium

Title: Journey through the past: Computational techniques to unveil plant genome evolution

Time: Wed, Feb 8, 2012, 10am

Place: MPI für Molekulare Pflanzenphysiologie, Room 0.21 in The Box

Abstract:
With the number of plant genome sequences quickly growing, the need for a central repository increases. Hence, resources that collect data generated by different sequencing initiatives, in a uniform format, are becoming useful tools for data mining as well as powerful starting points for comparative analyses. Here PLAZA 2.5, a user-friendly platform that integrates 25 published plant genomes, will be presented. Besides the raw structural and functional annotation a variety of tools were run and results can be browsed through an intuitive website. Eg. all genes are grouped in gene families, for which multiple sequence alignments and phylogenetic trees are readily available, along with a variety of other tools. To allow users to efficiently explore the wealth of data contained in PLAZA 2.5, various custom visualizations have been developed. This allows even complex data, combining various types of information, to be presented in a comprehensible way.

A second part of the platform is dedicated to study genome evolution. Both rearrangements after speciation and the effects of ancient large-scale duplications can be studied. Regions derived from a common ancestor, essential to study evolution at the genomic level, were detected based on the conservation of gene content and order using i-ADHoRe 3.0 (a new version specifically designed for such large-scale datasets). PLAZA 2.5 and i-ADHoRe 3.0 therefore are useful tools for plant researchers worldwide and shows how modern large-scale approaches can be used for efficiently studying genome evolution in plants. (PLAZA 2.5 is available from http://bioinformatics.psb.ugent.be/plaza/. i-ADHoRe 3.0 can be downloaded from http://bioinformatics.psb.ugent.be/software/. Both tools are free for academic use.)

Back to the seminar schedule



Past NLD Seminars (1994-2007) & (2008 ...)

Students' seminar: Theoretical Physics, PIK, Modeling & TSA Berlin-Potsdam-Colloquia: PhysGesellschaft Berlin, TU Berlin, Pro Physik, AIP, AEI, MPI-KGF, GFZ, HMI, PIK, AWI, Max Planck Institute for the History of Science, Mathematik, DPG Disputationen, & Vorschau UP

Udo Schwarz, Zentrum für Dynamik komplexer Systeme,
Universität Potsdam, Campus Golm Karl-Liebknecht-Str. 24, 14476 Potsdam, building 28, room 2.107
Phone: (+49-331) 977-1658, Fax : (+49-331) 977-1045

Email: Udo.Schwarz AT uni-potsdam.de

DFG SFB 1294

DFG Sonderforschungsbereich 1294 Data assimilation

DFG SPP 1488

DFG Schwerpunktprogramm 1488 Planetmag


News: odeint C++ library

Check out boost::odeint – our fast and flexible C++ library for integrating differential equations!