Content
ncRNAs are a large class of coding sequences that have a variety of functions that is determined mostly by their two-dimensional structure. In the last 10 years the more and more scientific discoveries have been made about various classes of RNA and following this growing importance more and more computational methods are being developed to search and classify those molecules. We will focus in this seminar on algorithmic methods to compute structures of RNA, compare RNAs combined on sequence and structure level and search them quicklt in large collections of genomics sequence.
Information for students
This is a classical seminar. Prof. Marsico will give an overview about the topic on the first date. Prof. Reinert an introduction into RNA folding on the second.
The students have to give a seminar talk of about 45-60 minutes about their topic. The seminar talks can be blocked towards the end of the semester. The language of the seminar is English and to pass the seminar you need to do the following:
- attend almost all the classes (if you miss more than one class you will be asked to write a report about a topic of your choice presented in the seminar class)
- give an oral presentation about a paper of your choice selected from the proposed list below. You will be asked for 3 choices and be assigned one in case of conflicts.
- Meet at least one week before your presentation with one of the instructors to present a first version.
- Each students is expected to participate actively in the discussion following the presentation by asking at least two questions regarding the presented topic and reviewing the other students' work (e.g. feedback on the talk and quality of the presentation)
Topics and papers
In the following table you find a set of minimum reading material. Depending on the number of participants this might be expanded. In addition you find here the introductionary material.
Paper assignment:
| Student | Paper |
| Arniella | Finding the most significant sequence and structure motifs in a set of RNA sequences |
| Bertrandt | Lightweight comparison of RNAs based on exact sequence–structure matches |
| Althoff | Query-Dependent Banding (QDB) for Faster RNA Similarity Searches |
| Wellner | A fast structural multiple alignment method for long RNA sequences |
| Grahl | Structator: fast index-based search for RNA sequence-structure patterns |
| Driller | Systematic discovery of structural elements governing stability of mammalian messenger RNAs |
| Adas | GraphClust: alignment-free structural clustering of local RNA secondary structures |
| Walde | Alignment of RNA base pairing probability matrices |
| Mohanakrishnan | RNAshapes: an integrated RNA analysis package based on abstract shapes |
| Jahnel | GraphProt: modeling binding preferences of RNA-binding proteins |
| Budzyak | Accurate multiple sequence-structure alignment of RNA sequences using combinatorial optimization |
| Krannich | GraphClust: alignment-free structural clustering of local RNA secondary structures (free) |
| Seiler | Annotating RNA motifs in sequences and alignments |
| Pockrandt | Fast online and index-based algorithms for approximate search of RNA sequence-structure patterns |
| Vavadar | Widespread purifying selection on RNA structure in mammals |