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P136 - GCB 2008 - German Conference on Bioinformatics 2008

https://dl.gi.de/handle/20.500.12116/21204
Auflistung nach:

Auflistung P136 - GCB 2008 - German Conference on Bioinformatics 2008 nach Autor:in "Backofen, Rolf"

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  • Konferenzbeitrag
    Lightweight Comparison of RNAs Based on Exact Sequence-Structure Matches
    (German Conference on Bioinformatics, 2008) Heyne, Steffen; Will, Sebastian; Beckstette, Michael; Backofen, Rolf
    Specific functions of RNA molecules are often associated with different motifs in the RNA structure. The key feature that forms such an RNA motif is the combination of sequence and structure properties. In this paper we introduce a new RNA sequence-structure comparison method which maintains exact matching substructures. Existing common substructures are treated as whole unit while variability is allowed between such structural mo- tifs. Based on a fast detectable set of overlapping and crossing substructure matches for two nested RNA secondary structures, our method computes the longest colinear sequence of substructures common to two RNAs in O(n2m2) time and O(nm) space. Applied to different RNAs, our method correctly identifies sequence-structure similarities between two RNAs. The results of our experiments are in good agreement with existing alignment-based meth- ods, but can be obtained in a fraction of running time, in particular for larger RNAs. The proposed algorithm is implemented in the program expaRNA, which is available from our website (www.bioinf.uni-freiburg.de/Software).
  • Konferenzbeitrag
    Structure Local Multiple Alignment of RNA
    (German Conference on Bioinformatics, 2008) Otto, Wolfgang; Will, Sebastian; Backofen, Rolf
    Today, RNA is well known to perform important regulatory and catalytic function due to its distinguished structure. Consequently, state-of-the-art RNA multiple alignment algorithms consider structure as well as sequence information. However, existing tools neglect the important aspect of locality. Notably, locality in RNA occurs as similarity of subsequences as well as similarity of only substructures. We present a novel approach for multiple alignment of RNAs that deals with both kinds of locality. The approach extends LocARNA by structural locality for computing all- against-all pairwise, structural local alignments. The final construction of the multiple alignments from the pairwise ones is delegated to T-Coffee. The paper systematically investigates structural locality in known RNA families. Benchmarking multiple align- ment tools on structural local families shows the need for algorithmic support of this locality. The improvement in accuracy in special cases is achieved while staying competitive with state-of-the-art alignment tools across the whole Bralibase. LocARNA and its T-Coffee extended variant LocARNATE are freely available at http://www.bioinf.uni-freiburg.de/Software/LocARNA/.