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  A polyhedral approach to RNA sequence structure alignment

Lenhof, H.-P., Reinert, K., & Vingron, M. (1998). A polyhedral approach to RNA sequence structure alignment. In S. Istrail, P. Pevzner, & M. Waterman (Eds.), Proceedings of the 2nd Annual International Conference on Computational Molecular Biology (RECOMB-98) (pp. 153-162). New York, USA: ACM Press.

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Datensatz-Permalink: https://hdl.handle.net/11858/00-001M-0000-000F-3761-4 Versions-Permalink: https://hdl.handle.net/11858/00-001M-0000-000F-3762-2
Genre: Konferenzbeitrag

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 Urheber:
Lenhof, Hans-Peter1, Autor           
Reinert, Knut1, Autor           
Vingron, Martin, Autor
Affiliations:
1Algorithms and Complexity, MPI for Informatics, Max Planck Society, ou_24019              

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Schlagwörter: -
 Zusammenfassung: Ribonucleic acid (RNA) is a polymer composed of four bases denoted A, C, G, and U. It is a generally single-stranded molecule where the bases form hydrogen bonds within the same molecule leading to structure formation. In comparing different homologous RNA molecules it is important to consider both the base sequence and the structure of the molecules. Traditional alignment algorithms can only account for the sequence of bases, but not for the base pairings. Considering the structure leads to significant computational problems because of the dependencies introduced by the base pairings. In this paper we address the problem of optimally aligning a given RNA sequence of unknown structure to one of known sequence and structure. We phrase the problem as an integer linear program and then solve it using methods from polyhedral combinatorics. In our computational experiments we could solve large problem instances -- 23S ribosomal RNA with more than $1400$ bases -- a size intractable for former algorithms.

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Sprache(n): eng - English
 Datum: 2010-03-021998
 Publikationsstatus: Erschienen
 Seiten: -
 Ort, Verlag, Ausgabe: New York, USA : ACM Press
 Inhaltsverzeichnis: -
 Art der Begutachtung: -
 Identifikatoren: eDoc: 517921
Anderer: Local-ID: C1256428004B93B8-D9EBAC8904160ABEC12565D90043268B-LenReiVin98
 Art des Abschluß: -

Veranstaltung

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Titel: Untitled Event
Veranstaltungsort: New York, USA
Start-/Enddatum: 1998

Entscheidung

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Titel: Proceedings of the 2nd Annual International Conference on Computational Molecular Biology (RECOMB-98)
Genre der Quelle: Konferenzband
 Urheber:
Istrail, Sorin, Herausgeber
Pevzner, Pavel, Herausgeber
Waterman, Michael, Herausgeber
Affiliations:
-
Ort, Verlag, Ausgabe: New York, USA : ACM Press
Seiten: - Band / Heft: - Artikelnummer: - Start- / Endseite: 153 - 162 Identifikator: ISBN: 0-89791-976-9