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A Common Framework for Linear and Cyclic Multiple Sequence Alignment Problems

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Book cover Algorithms in Bioinformatics (WABI 2014)

Part of the book series: Lecture Notes in Computer Science ((LNBI,volume 8701))

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Abstract

Circularized RNAs have received considerable attention is the last few years following the discovery that they are not only a rather common phenomenon in the transcriptomes of Eukarya and Archaea but also may have key regulatory functions. This calls for the adaptation of basic tools of sequence analysis to accommodate cyclic sequences. Here we discuss a common formal framework for linear and circular alignments as partitions that preserve (cyclic) order. We focus on the similarities and differences and describe a prototypical ILP formulation.

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Author information

Authors and Affiliations

  1. Dept. Computer Science, and Interdisciplinary Center for Bioinformatics, Univ. Leipzig, Härtelstr. 16-18, Leipzig, Germany

    Sebastian Will & Peter F. Stadler

  2. MPI Mathematics in the Sciences, Inselstr. 22, Leipzig, Germany

    Peter F. Stadler

  3. FHI Cell Therapy and Immunology, Perlickstr. 1, Leipzig, Germany

    Peter F. Stadler

  4. Dept. Theoretical Chemistry, Univ. Vienna, Währingerstr. 17, Wien, Austria

    Peter F. Stadler

  5. Bioinformatics and Computational Biology research group, University of Vienna, A-1090 Währingerstraße 17, Vienna, Austria

    Peter F. Stadler

  6. RTH, Univ. Copenhagen, Grønnegårdsvej 3, Frederiksberg C, Denmark

    Peter F. Stadler

  7. Santa Fe Institute, 1399 Hyde Park Rd., Santa Fe, USA

    Peter F. Stadler

Authors
  1. Sebastian Will
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  2. Peter F. Stadler
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Editor information

Editors and Affiliations

  1. David R. Cheriton School of Computer Science, University of Waterloo, ON, Canada

    Dan Brown

  2. Institute of Microbiology and Genetics, Department of Bioinformatics, University of Göttingen, Germany, Goldschmidtstr. 1, 37077, Göttingen, Germany

    Burkhard Morgenstern

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Will, S., Stadler, P.F. (2014). A Common Framework for Linear and Cyclic Multiple Sequence Alignment Problems. In: Brown, D., Morgenstern, B. (eds) Algorithms in Bioinformatics. WABI 2014. Lecture Notes in Computer Science(), vol 8701. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-662-44753-6_11

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  • DOI: https://doi.org/10.1007/978-3-662-44753-6_11

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-662-44752-9

  • Online ISBN: 978-3-662-44753-6

  • eBook Packages: Computer ScienceComputer Science (R0)

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