Phylogenetic profiling SS 2007

Max Planck Institute for Molecular Genetics - Ihnestra§e 63-73 - 14195 Berlin - Germany - Phone: (+49 30) 8413 0 - Fax: (+49 30) 8413 1394

Max Planck Institute for Molecular Genetics - Ihnestraße 63-73 - 14195 Berlin - Germany -
Phone: (+49 30) 8413 1150 - Fax: (+49 30) 8413 1394

Project Phylogenetic profiles

We can use phylogenetic profiles to predict protein-protein interaction and protein function. The large number of completely sequenced genomes have enhanced the power of the method. The course will focus on prokaryotes and compare the various approaches that can be used to extract a maximum of information. The determination of orthologous, predictions of function and validation will be studied compared. The programming can be performed in Python or Java or another common language agreed upon.

Meetings

First meeting (Vorbesprechung)
Thursday, February 21th, 2008, 11am (tentative, please wait for confirmation)

Begleitseminar
To be determined, probably mid March. All meetings will be held in seminar room 331, 3rd floor, MPI for Molecular Genetics, Ihnestr. 73.

Literature

All publications are available without restrictions.

Pellegrini, M, et al. Assigning protein functions by comparative genome analysis: protein phylogenetic profiles.
Tatutsov RL, et al. The COG database: a tool for genome-scale analysis of protein functions and evolution.
Doerks T, et al. Functional clues for hypothetical proteins based on genomic context analysis in prokaryotes
Medini et al. Protein Homology Network Families Reveal Step-Wise Diversification of Type III and Type IV Secretion Systems
Tettelin, H et al. Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: Implications for the microbial pan-genome

Lecturers

Prof. Martin Vingron
(vingron@molgen.mpg.de)
Dr. Roland Krause
(krause@molgen.mpg.de)

Last update 2008-02-14