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Author, Editor

Author(s):

Lenhof, Hans-Peter
Reinert, Knut
Vingron, Martin

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Editor(s):

Istrail, Sorin
Pevzner, Pavel
Waterman, Michael

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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

URL of the conference:

http://www.mssm.edu/biomath/recomb98.html

URL for downloading the paper:


Event Address*:

New York, USA

Language:

English

Event Date*
(no longer used):

March 22-25

Organization:

Association of Computing Machinery (ACM)

Event Start Date:

16 September 2019

Event End Date:

16 September 2019

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



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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
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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