DFG-Projekt: A Flexible and Efficient System for the Detection of RNA Sequence/Structure Motifs

Description of the project:
In this project, we concentrate on algorithmic approaches for the comparison of RNAs. The comparison of RNAs requires to consider both the sequence and structure of the RNAs. We want to overcome the limitations of existing approaches in both expressivity and efficiency. We will investigate three directions: 1. We will study different means for improving the quality of RNA alignment algorithms. Thus, we will study different types of local RNA alignment algorithms (both sequence locality and a more recent new notion called structure locality), since RNA motifs are of local nature. Furthermore, we will consider an important class of structures (pseudoknots) usually not handled by RNA alignment tools. 2. Current RNA alignment algorithms are too time costly. We propose to study how different optimization techniques successfully applied to sequence alignment can be used in RNA alignment. 3. We will also perform tasks required for the success in practical applications. Thus, we plan to develop new filtering techniques for fast search of RNA motifs in genome databases, which is a necessary prerequisite to promote research on functional RNAs. We wsill investigate approaches for improving progressive multiple RNA alignment, and will train parameters on benchmark sets. This will also allow us to investigate the properties of the introduced scoring. Since any development will be incorporated into our widely used multiple alignment system LocARNA, this will produce one of the most advanced system for defining and searching various types of RNA motifs.

contact person: Mathias Möhl
Email: mmohl@informatik.uni-freiburg.de
Start of project: 2009
End of project: 2012
Project Management:
Albert-Ludwigs-University Freiburg
Prof. Dr. Rolf Backofen
Prof. Dr. Rolf Backofen
Georges-Köhler-Allee 106
79110 Freiburg

Phone: +49 (0) 761-203-7461
Fax: +49 (0) 761-203-7462
Email: backofen@informatik.uni-freiburg.de
Actual Research Report
  • DFG