Journal Article
@Article
Artikel in Fachzeitschrift


Show entries of:

this year (2019) | last year (2018) | two years ago (2017) | Notes URL

Action:

login to update

Options:








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

Journal's URL:


Download URL
for the article:


Language:

English

Publisher

Publisher's
Name:


Publisher's URL:


Publisher's
Address:


ISSN:


Vol, No, pp, Date

Volume*:

5

Number:

3

Publishing Date:

1998

Pages*:

517-530

Number of
VG Pages:


Page Start:


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.

URL for the Abstract:


Categories,
Keywords:

Computational Biology, Branch-and-Cut, Structural Alignment

HyperLinks / References / URLs:


Copyright Message:


Personal Comments:


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:

@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
Show details for Edit History (please click the blue arrow to see the details)Edit History (please click the blue arrow to see the details)
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
01/21/1999 02:24:20 PM
Revision
0.



Editor
Knut Reinert



Edit Date