To keep you up to date with the latest developments in virus bioinformatics, especially new tools that might help you in your research, the European Virus Bioinformatics Center is organising a monthly lecture series entitled viruses in silico.
The lecture will take place online as a Zoom Meeting. Participation is free. Use the registration form to receive the login details. Registration is possible until 1 hour before the start of the event.
Lectures are not recorded.
Computational identification of highly conserved, structured functional modules in long RNA molecules.
27. March 2023 | 04 pm CET
Tomasz Krzysztof Wirecki, International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland
The majority of viruses that infect humans and other organisms, have Ribonucleic Acid (RNA) genomes. The structural elements of mRNA molecules have regulatory functions in both the untranslated (UTR) and coding (CDS) regions of viral genomes. Local secondary structures that are evolutionarily conserved in CDSs have been shown to be functional, and evidence suggests that these structures constitute an evolutionarily conserved level of functional organization in viruses.
We propose to identify highly conserved structured functional modules in positive-sense viral RNA (++ssRNA) genome sequences, including both UTRs and CDSs, and group them based on their sequence-structure relationship using theoretical studies and structural biology. We have developed a novel computational approach to search for highly conserved, structured functional modules in long RNA molecules.
Our prototype program uses a sliding window approach to carry out secondary structure predictions and utilizes various structure predictors to generate local structures. The procedure allows for the determination of stably structured regions, and finally, all robustly folded structures for the whole sequence are reported. We present the software benchmark results based on structures we previously reported for SARS-CoV-2. Additionally, we show initial results of identifying potentially conserved structural modules in other viral taxa.
|24. April 2023||Masayuki Horie, Osaka Metropolitan University, Japan|
|May 2023||ViBioM 2023|
|July 2023||ICTV/EVBC symposium on Automating Virus Taxonomy|
|28. August 2023||Dominik Heider, University of Marburg, Germany|
|23. October 2023||Gabriel da Luz Wallau, Bernhard Nocht Institute for Tropical Medicine, Germany|
|postponed||Mart Krupovic, Institut Pasteur, France|