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Auflistung nach Autor:in "Tafer, Hakim"

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  • Konferenzbeitrag
    RNAplex: a fast and flexible RNA-RNA interaction search tool
    (German conference on bioinformatics – GCB 2007, 2007) Tafer, Hakim; Hofacker, Ivo L.
    Regulatory RNAs often unfold their action via RNA-RNA interaction. Transcriptional gene silencing by means of siRNAs and miRNA as well as snoRNA directed RNA editing rely on this mechanism. ncRNA regulation in bacteria is mainly based upon RNA duplex formation. Finding putative target sites for newly discovered ncR-NAs is a lengthy task as tools for cofolding RNA molecules like RNAcofold and RNAup have a run time proportional to O((n + m)3) which makes them unpractical for whole genome search. We present a new program, RNAplex, especially designed to quickly find possible hybridization sites for a query RNA in large RNA databases. In contrast to earlier approaches, RNAplex uses a slightly different energy model which reduces the computational time by a factor 65 compared to RNAhybrid without loss of sensitivity.
  • 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.