Bioinformatics and Evolutionary Genomics 2017 A course for Master-students and PhD-students

March 6 till March 17.


Organizer: Prof. Dr. B. Snel, Theoretical Biology and Bioinformatics, Department of Biology, Utrecht University

Reading and discussing primary literature where bioinformatic methods are a main component of arriving at the biological results. This includes classic papers as well as recent papers. Pen and paper assignments on questions and papers. Preparing critique questions against a paper and prepare to defend a paper. Becoming (by practice) familiar with basic linux and command line application of bioinformatic tools. Collecting homologs and homologous regions of proteins (hmmer/ blast), constructing multiple sequence alignments (mafft / clustal) and making phylogenetic trees (raxml/nj). Distant homology for orthology prediction. Distant homolgoy in relation to domain prediction (pfam/hmmer command line) and domain/protein evolution. Orthology small scale via annotating phylogenetic trees. Recognizing horizontal gene transfer / endosymbiotic gene transfer in gene trees. Protein interactions. Evolution of protein interactions and pathways. Large scale orthology: methods and databases. The outlines of the eukaryotic tree of life (ToL), the animal ToL, the fungal ToL, and the plant tree of life. Recognizing genome duplications and consequences of genome duplications.


Exercises: here

Articles: here

Slides of the Lectures: here

colprot.par for clustal: here