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Auflistung nach Schlagwort "dynamic programming"

1 - 2 von 2
  • Konferenzbeitrag
    Comparative analysis of cyclic sequences: Viroids and other small circular RNAs
    (German Conference on Bioinformatics, 2006) Mosig, Axel; Hofacker, Ivo L.; Stadler, Peter F.
    The analysis of small circular sequences requires specialized tools. While the differences between linear and circular sequences can be neglected in the case of long molecules such as bacterial genomes since in practice all analysis is performed in sequence windows, this is not true for viroids and related sequences which are usually only a few hundred basepairs long. In this contribution we present basic algorithms and corresponding software for circular RNAs. In particular, we discuss the problem of pairwise and multiple cyclic sequence alignments with affine gap costs, and an extension of a recent approach to circular RNA folding to the computation of consensus structures.
  • Konferenzbeitrag
    Thermodynamics of RNA-RNA binding
    (German Conference on Bioinformatics 2005 (GCB 2005), 2005) Mückstein, Ulrike; Tafer, Hakim; Hackermüller, Jörg; Bernhart, Stephan H.; Stadler, Peter F.; Hofacker, Ivo L.
    We present an extension of the standard partition function approach to RNA secondary structures that computes the probabilities Pu[i, j] that a sequence interval [i, j] is unpaired. Comparison with experimental data shows that Pu[i, j] can be applied as a significant determinant of local target site accessibility for RNA interference (RNAi). Furthermore, these quantities can be used to rigorously determine binding free energies of short oligomers to large mRNA targets. The resource consumption is comparable to a single partition function computation for the large target molecule. We can show that RNAi efficiency correlates well with the binding probabilities of siRNAs to their respective mRNA target.