Seminar: On Gene Linkages, RNA Secondary Structure Prediction and Searching for Non-coding RNAs

2011-05-23: By Christian Höner zu Siederdissen, University of Vienna, Austria. At 14:00, University of Copenhagen, LIFE, Grønnegårdsvej 3, Building 1-61, Library 2nd Floor, 1870 Frederiksberg C.

Registration is not necessary. Refreshments will be served.


In this overview talk, three topics are being discussed: (i) gene linkage prediction, (ii) structure prediction of non-coding RNA (iii) and the search for non-coding RNA.

(i) Linked genes: Biological molecules may interact tightly and therefore co-evolve as well. We provide means of discovering linkages between non-coding RNA and/or protein-coding regions in genomes among metazoa. As a result, probable linkages can be traced throughout species and first occurances of linkage be determined.

(ii) Structure prediction: the Vienna RNA package has been one of the most widely used tools for RNA secondary structure prediction in recent years. We extended the idea of RNA secondary structure prediction as given by RNAfold to include biologically relevant features, that have largely been neglegted but are necessary for the correct function of the RNA, while still remaining in the realm of efficient algorithms.

(iii) Search for non-coding RNA: HMMER and Infernal are de-facto gold standards in the search for homologuous protein and ncRNA sequences in different genomes. The talk will close with some examples of why results have to be evaluated carefully. Methods to increase sensitivity and specificity of genome-wide searches will be presented in an informal manner.

Co-authors include: Manja Marz, Stephan H Bernhart, Robert Giegerich, Ivo L Hofacker, and Peter F Stadler