de.mpg.escidoc.pubman.appbase.FacesBean
Deutsch
 
Hilfe Wegweiser Datenschutzhinweis Impressum Kontakt
  DetailsucheBrowse

Datensatz

DATENSATZ AKTIONENEXPORT

Freigegeben

Zeitschriftenartikel

A Polyhedral Approach to RNA Sequence Structure Alignment

MPG-Autoren
http://pubman.mpdl.mpg.de/cone/persons/resource/persons44909

Lenhof,  Hans-Peter
Algorithms and Complexity, MPI for Informatics, Max Planck Society;

http://pubman.mpdl.mpg.de/cone/persons/resource/persons45277

Reinert,  Knut
Algorithms and Complexity, MPI for Informatics, Max Planck Society;

Externe Ressourcen
Es sind keine Externen Ressourcen verfügbar
Volltexte (frei zugänglich)
Es sind keine frei zugänglichen Volltexte verfügbar
Ergänzendes Material (frei zugänglich)
Es sind keine frei zugänglichen Ergänzenden Materialien verfügbar
Zitation

Lenhof, H.-P., Reinert, K., & Vingron, M. (1998). A Polyhedral Approach to RNA Sequence Structure Alignment. Journal of Computational Biology, 5(3), 517-530.


Zitierlink: http://hdl.handle.net/11858/00-001M-0000-000F-3763-F
Zusammenfassung
Ribonucleic acid (RNA) is a polymer composed of four bases denoted A, C, G, and U. It generally is a single-stranded molecule where the bases form hydrogen bonds w ithin 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.