Pure multiple RNA secondary structure alignments: A progressive profile approach

Höchsmann M, Voss B, Giegerich R (2004)
IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATIOCS 1(1): 53-62.

Zeitschriftenaufsatz | Veröffentlicht | Englisch
 
Download
Es wurde kein Volltext hochgeladen. Nur Publikationsnachweis!
Autor/in
; ;
Abstract / Bemerkung
In functional, noncoding RNA, structure is often essential to function. While the full 3D structure is very difficult to determine, the 2D structure of an RNA molecule gives good clues to its 3D structure, and for molecules of moderate length, it can be predicted with good reliability. Structure comparison is, in analogy to sequence comparison, the essential technique to infer related function. We provide a method for computing multiple alignments of RNA secondary structures under the tree alignment model, which is suitable to cluster RNA molecules purely on the structural level, i.e., sequence similarity is not required. We give a systematic generalization of the profile alignment method from strings to trees and forests. We introduce a tree profile representation of RNA secondary structure alignments which allows reasonable scoring in structure comparison. Besides the technical aspects, an RNA profile is a useful data structure to represent multiple structures of RNA sequences. Moreover, we propose a visualization of RNA consensus structures that is enriched by the full sequence information.
Stichworte
RNA secondary structures; alignment of trees; noncoding RNAs
Erscheinungsjahr
2004
Zeitschriftentitel
IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATIOCS
Band
1
Ausgabe
1
Seite(n)
53-62
ISSN
1545-5963
Page URI
https://pub.uni-bielefeld.de/record/1600293

Zitieren

Höchsmann M, Voss B, Giegerich R. Pure multiple RNA secondary structure alignments: A progressive profile approach. IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATIOCS. 2004;1(1):53-62.
Höchsmann, M., Voss, B., & Giegerich, R. (2004). Pure multiple RNA secondary structure alignments: A progressive profile approach. IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATIOCS, 1(1), 53-62. doi:10.1109/TCBB.2004.11
Höchsmann, M., Voss, B., and Giegerich, R. (2004). Pure multiple RNA secondary structure alignments: A progressive profile approach. IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATIOCS 1, 53-62.
Höchsmann, M., Voss, B., & Giegerich, R., 2004. Pure multiple RNA secondary structure alignments: A progressive profile approach. IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATIOCS, 1(1), p 53-62.
M. Höchsmann, B. Voss, and R. Giegerich, “Pure multiple RNA secondary structure alignments: A progressive profile approach”, IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATIOCS, vol. 1, 2004, pp. 53-62.
Höchsmann, M., Voss, B., Giegerich, R.: Pure multiple RNA secondary structure alignments: A progressive profile approach. IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATIOCS. 1, 53-62 (2004).
Höchsmann, Matthias, Voss, Björn, and Giegerich, Robert. “Pure multiple RNA secondary structure alignments: A progressive profile approach”. IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATIOCS 1.1 (2004): 53-62.

Export

Markieren/ Markierung löschen
Markierte Publikationen

Open Data PUB

Web of Science

Dieser Datensatz im Web of Science®

Quellen

PMID: 17048408
PubMed | Europe PMC

Suchen in

Google Scholar