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Auflistung nach Autor:in "Mosig, Axel"

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  • 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
    Tanimoto’s Best Barbecue: Discovering Regulatory Modules using Tanimoto Scores
    (German conference on bioinformatics – GCB 2007, 2007) Menzel, Peter; Stadler, Peter F.; Mosig, Axel
    We present a combinatorial method for discovering cis-regulatory modules in promoter sequences. Our approach combines “sliding window” approaches with a scoring function based on the so-called Tanimoto score. This allows to identify sets of binding sites that tend to occur preferentially in the vicinity of each other in a given set of promoter sequences belonging to co-expressed or orthologous genes. We bench- mark our method on a data set derived from muscle-specific genes, demonstrating that our approach is capable of identifying modules that were identified as functional in previous studies.