Homology Search with Fragmented Nucleic Acid Sequence Patterns.pdfVIP

Homology Search with Fragmented Nucleic Acid Sequence Patterns Axel Mosig18, Julian J.-L. Chen23, and Peter F. Stadler4567 1 Department of Combinatorics and Geometry (DCG), CAS-MPG Partner Institute for Computational Biology (PICB), Shanghai Institutes for Biological Sciences (SIBS) Campus, Shanghai, China axel@ 2 School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA jlchen@ 3 Department of Chemistry and Biochemistry, Arizona State University, Tempe, AZ 85287, USA 4 Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, University of Leipzig, H¨artelstraße 16-18, D-04107 Leipzig, Germany; 5 RNomics Group, Fraunhofer Institut f¨ur Zelltherapie und Immunologie — IZI Deutscher Platz 5e, D-04103 Leipzig, Germany; 6 Department of Theoretical Chemistry, University of Vienna, W¨ahringerstraße 17, A-1090 Wien, Austria; 7 Santa Fe Institute, 1399 Hyde Park Rd., Santa Fe, NM 87501, USA studla@bioinf.uni-leipzig.de 8 Max Planck Institute for Mathematics in the Sciences, Inselstraße 22, D-04103 Leipzig, Germany Abstract. The comprehensive annotation of non-coding RNAs in newly sequenced genomes is still a largely unsolved problem because many func- tional RNAs exhibit not only poorly conserved sequences but also large variability in structure. In many cases, such as Y RNAs, vault RNAs, or telomerase RNAs, sequences differ by large insertions or deletions and have only a few small sequence patterns in common. Here we present fragrep2, a