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| Accurate multiple sequence-structure alignment of RNA sequences using combinatorial optimization Bauer, Markus |
| Haupttitel | Accurate multiple sequence-structure alignment of RNA sequences using combinatorial optimization |
| Autor | Bauer, Markus; Klau, Gunnar W.; Reinert, Knut |
| Seitenzahl | 30 S. |
| Schriftenreihe | Freie Universität Berlin, Fachbereich Mathematik und Informatik : Ser. B, Informatik ; [20]07,06 |
| Fachbereich/Einrichtung | FB Mathematik und Informatik |
| Arbeitsbereich/Institut | Institut für Informatik |
| Erscheinungsjahr | 2007 |
| Dokumente | pdf-Datei
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| DDC | 005 Programmierung, Programme, Daten |
| Dokumententyp/-Sammlungen | Report |
| Medientyp/Format | Text |
| Abstract | Background: The discovery of functional non-coding RNA sequences has led to an increasing interest in algorithms related to RNA analysis. Traditional sequence alignment algorithms, however, fail at computing reliable alignments of low-homology RNA sequences. The spatial conformation of RNA sequences largely determines their function, and therefore RNA alignment algorithms have to take structural information into account. Results: We present a graph-based representation for sequence-structure alignments, which we model as an integer linear program (ILP). We sketch how we compute an optimal or near-optimal solution to the ILP using methods from combinatorial optimization, and present results on a recently published benchmark set for RNA alignments. Conclusions: The implementation of our algorithm yields better alignments in terms of two published scores than the other programs that we tested: This is especially the case with an increasing number of input sequences. Our program LaRA is freely available from http://www.planet-lisa.net. |
| Sprache | Englisch |
| Rechte | Nutzungsbedingungen |
| Zugriffstatistik | |
| Statische URL | http://edocs.fu-berlin.de/docs/receive/FUDOCS_document_000000003915 |
| Erstellt am | 14.10.2009 - 14:38:05 |
| Letzte Änderung | 04.04.2013 - 09:33:25 |
