MPI-INF Logo
Publications

Server    domino.mpi-inf.mpg.de

Proceedings Article, Paper
@InProceedings
Beitrag in Tagungsband, Workshop

Author, Editor
Author(s):
Lenhof, Hans-Peter
Reinert, Knut
Vingron, Martin
dblp
dblp
dblp
Editor(s):
Istrail, Sorin
Pevzner, Pavel
Waterman, Michael
dblp
dblp
dblp
BibTeX cite key*:
LenReiVin98
Title, Booktitle
Title*:
A polyhedral approach to RNA sequence structure alignment
Booktitle*:
Proceedings of the 2nd Annual International Conference on Computational Molecular Biology (RECOMB-98)
Event, URLs
Conference URL::
http://www.mssm.edu/biomath/recomb98.html
Downloading URL:
Event Address*:
New York, USA
Language:
English
Event Date*
(no longer used):
March 22-25
Organization:
Association of Computing Machinery (ACM)
Event Start Date:
31 October 2020
Event End Date:
31 October 2020
Publisher
Name*:
ACM Press
URL:
Address*:
New York, USA
Type:
Vol, No, Year, pp.
Series:
Volume:
Number:
Month:
March
Pages:
153-162
Year*:
1998
VG Wort Pages:
ISBN/ISSN:
0-89791-976-9
Sequence Number:
DOI:
Note, Abstract, ©
(LaTeX) Abstract:
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.
Keywords:
Computational Biology, Combinatorial Optimization
Download
Access Level:

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



BibTeX Entry:

@INPROCEEDINGS{LenReiVin98,
AUTHOR = {Lenhof, Hans-Peter and Reinert, Knut and Vingron, Martin},
EDITOR = {Istrail, Sorin and Pevzner, Pavel and Waterman, Michael},
TITLE = {A polyhedral approach to {RNA} sequence structure alignment},
BOOKTITLE = {Proceedings of the 2nd Annual International Conference on Computational Molecular Biology (RECOMB-98)},
PUBLISHER = {ACM Press},
YEAR = {1998},
ORGANIZATION = {Association of Computing Machinery (ACM)},
PAGES = {153--162},
ADDRESS = {New York, USA},
MONTH = {March},
ISBN = {0-89791-976-9},
}


Entry last modified by Evelyn Haak, 03/02/2010
Hide details for Edit History (please click the blue arrow to see the details)Edit History (please click the blue arrow to see the details)

Editor(s)
Knut Reinert
Created
04/01/1998 02:13:27 PM
Revisions
3.
2.
1.
0.
Editor(s)
Evelyn Haak
Uwe Brahm
Uwe Brahm
Knut Reinert
Edit Dates
01/04/99 13:08:29
29.03.99 18:57:04
29.03.99 18:56:22
01/04/98 13:13:28