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Author, Editor(s)
Author(s):
Lenhof, Hans-Peter
Reinert, Knut
Vingron, Martin		dblp
dblp
dblp

BibTeX cite key*:

LenReiVin1998

Title

Title*:

A Polyhedral Approach to RNA Sequence Structure Alignment

Journal

Journal Title*:

Journal of Computational Biology
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Language:

English

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Name:


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ISSN:


Vol, No, pp, Date

Volume*:

5
Number:

3

Publishing Date:

1998

Pages*:

517-530
Number of
VG Pages:


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Page End:


Sequence Number:


DOI:


Note, Abstract, ©

Note:


(LaTeX) Abstract:

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.

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Categories,
Keywords:

Computational Biology, Branch-and-Cut, Structural Alignment

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MPG Unit:
Max-Planck-Institut für Informatik
MPG Subunit:
Algorithms and Complexity Group
Audience:
experts only
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MPII WWW Server, MPII FTP Server, MPG publications list, university publications list, working group publication list, Fachbeirat


BibTeX Entry:

@ARTICLE{LenReiVin1998,
AUTHOR = {Lenhof, Hans-Peter and Reinert, Knut and Vingron, Martin},
 TITLE = {A Polyhedral Approach to RNA Sequence Structure Alignment},
 JOURNAL = {Journal of Computational Biology},
 YEAR = {1998},
 NUMBER = {3},
 VOLUME = {5},
 PAGES = {517--530},
}

Entry last modified by Knut Reinert, 03/02/2010
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Editor(s)
Knut Reinert		Created
01/21/1999 14:24:20
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Editor
Knut Reinert



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