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Auflistung nach Autor:in "Otto, Wolfgang"

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  • Konferenzbeitrag
    NFDI4DS Shared Tasks
    (INFORMATIK 2023 - Designing Futures: Zukünfte gestalten, 2023) Abu Ahmad, Raia; Borisova, Ekaterina; Rehm, Georg; Dietze, Stefan; Kamakar, Saurav; Otto, Wolfgang; D’Souza, Jennifer; Limani, Fidan; Usbeck, Ricardo
    Shared tasks have proven to be successful in proposing innovative solutions for challenging research problems. The NFDI4DS consortium plans to host various shared tasks to tackle problems under the umbrella of scholarly information processing. We discuss three shared tasks in detail: Field of Research Classification, Software Mention Detection, and Tracking State-of-the-Art in Empirical AI. We also briefly mention other shared tasks planned to be released in the future.
  • 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/.