Local similarity in RNA secondary structures.

Höchsmann M, Töller T, Giegerich R, Kurtz S (2003)
Proc IEEE Comput Soc Bioinform Conf 2: 159-168.

Zeitschriftenaufsatz | Veröffentlicht | Englisch
Es wurden keine Dateien hochgeladen. Nur Publikationsnachweis!
Höchsmann, Matthias; Töller, Thomas; Giegerich, RobertUniBi; Kurtz, Stefan
Abstract / Bemerkung
We present a systematic treatment of alignment distance and local similarity algorithms on trees and forests. We build upon the tree alignment algorithm for ordered trees given by Jiang et. al (1995) and extend it to calculate local forest alignments, which is essential for finding local similar regions in RNA secondary structures. The time complexity of our algorithm is O(|F(1)| |F(2) deg(F(1)) deg(F(2)) (deg(F(1)) + deg(F(2))) where |F(i)| is the number of nodes in forest F(i) and deg (F(i)) is the degree of F(i). We provide carefully engineered dynamic programming implementations using dense, two-dimensional tables which considerably reduces the space requirement. We suggest a new representation of RNA secondary structures as forests that allow reasonable scoring of edit operations on RNA secondary structures. The comparison of RNA secondary structures is facilitated by a new visualization technique for RNA secondary structure alignments. Finally, we show how potential regulatory motifs can be discovered solely by their structural preservation, and independent of their sequence conservation and position.
Proc IEEE Comput Soc Bioinform Conf
Page URI


Höchsmann M, Töller T, Giegerich R, Kurtz S. Local similarity in RNA secondary structures. Proc IEEE Comput Soc Bioinform Conf. 2003;2:159-168.
Höchsmann, M., Töller, T., Giegerich, R., & Kurtz, S. (2003). Local similarity in RNA secondary structures. Proc IEEE Comput Soc Bioinform Conf, 2, 159-168.
Höchsmann, M., Töller, T., Giegerich, R., and Kurtz, S. (2003). Local similarity in RNA secondary structures. Proc IEEE Comput Soc Bioinform Conf 2, 159-168.
Höchsmann, M., et al., 2003. Local similarity in RNA secondary structures. Proc IEEE Comput Soc Bioinform Conf, 2, p 159-168.
M. Höchsmann, et al., “Local similarity in RNA secondary structures.”, Proc IEEE Comput Soc Bioinform Conf, vol. 2, 2003, pp. 159-168.
Höchsmann, M., Töller, T., Giegerich, R., Kurtz, S.: Local similarity in RNA secondary structures. Proc IEEE Comput Soc Bioinform Conf. 2, 159-168 (2003).
Höchsmann, Matthias, Töller, Thomas, Giegerich, Robert, and Kurtz, Stefan. “Local similarity in RNA secondary structures.”. Proc IEEE Comput Soc Bioinform Conf 2 (2003): 159-168.

33 Zitationen in Europe PMC

Daten bereitgestellt von Europe PubMed Central.

Computational Approaches and Related Tools to Identify MicroRNAs in a Species: A Bird's Eye View.
Rajendiran A, Chatterjee A, Pan A., Interdiscip Sci 10(3), 2018
PMID: 28361256
Rice In Vivo RNA Structurome Reveals RNA Secondary Structure Conservation and Divergence in Plants.
Deng H, Cheema J, Zhang H, Woolfenden H, Norris M, Liu Z, Liu Q, Yang X, Yang M, Deng X, Cao X, Ding Y., Mol Plant 11(4), 2018
PMID: 29409859
DynaMIT: the dynamic motif integration toolkit.
Dassi E, Quattrone A., Nucleic Acids Res 44(1), 2016
PMID: 26253738
Studying RNA Homology and Conservation with Infernal: From Single Sequences to RNA Families.
Barquist L, Burge SW, Gardner PP., Curr Protoc Bioinformatics 54(), 2016
PMID: 27322404
Annotating RNA motifs in sequences and alignments.
Gardner PP, Eldai H., Nucleic Acids Res 43(2), 2015
PMID: 25520192
Web-Beagle: a web server for the alignment of RNA secondary structures.
Mattei E, Pietrosanto M, Ferrè F, Helmer-Citterich M., Nucleic Acids Res 43(w1), 2015
PMID: 25977293
STAR3D: a stack-based RNA 3D structural alignment tool.
Ge P, Zhang S., Nucleic Acids Res 43(20), 2015
PMID: 26184875
ExpaRNA-P: simultaneous exact pattern matching and folding of RNAs.
Otto C, Möhl M, Heyne S, Amit M, Landau GM, Backofen R, Will S., BMC Bioinformatics 15(), 2014
PMID: 25551362
Hyper conserved elements in vertebrate mRNA 3'-UTRs reveal a translational network of RNA-binding proteins controlled by HuR.
Dassi E, Zuccotti P, Leo S, Provenzani A, Assfalg M, D'Onofrio M, Riva P, Quattrone A., Nucleic Acids Res 41(5), 2013
PMID: 23376935
The impact of age, biogenesis, and genomic clustering on Drosophila microRNA evolution.
Mohammed J, Flynt AS, Siepel A, Lai EC., RNA 19(9), 2013
PMID: 23882112
Clustering rfam 10.1: clans, families, and classes.
Lessa FA, Raiol T, Brigido MM, Martins Neto DS, Walter ME, Stadler PF., Genes (Basel) 3(3), 2012
PMID: 24704975
Multi-scale RNA comparison based on RNA triple vector curve representation.
Li Y, Duan M, Liang Y., BMC Bioinformatics 13(), 2012
PMID: 23110635
Identifying and searching for conserved RNA localisation signals.
Hamilton RS, Davis I., Methods Mol Biol 714(), 2011
PMID: 21431757
Understanding the transcriptome through RNA structure.
Wan Y, Kertesz M, Spitale RC, Segal E, Chang HY., Nat Rev Genet 12(9), 2011
PMID: 21850044
ViennaRNA Package 2.0.
Lorenz R, Bernhart SH, Höner Zu Siederdissen C, Tafer H, Flamm C, Stadler PF, Hofacker IL., Algorithms Mol Biol 6(), 2011
PMID: 22115189
A bioinformatics search pipeline, RNA2DSearch, identifies RNA localization elements in Drosophila retrotransposons.
Hamilton RS, Hartswood E, Vendra G, Jones C, Van De Bor V, Finnegan D, Davis I., RNA 15(2), 2009
PMID: 19144907
A conserved 3' extension in unusual group II introns is important for efficient second-step splicing.
Stabell FB, Tourasse NJ, Kolstø AB., Nucleic Acids Res 37(10), 2009
PMID: 19304998
Strategies for measuring evolutionary conservation of RNA secondary structures.
Gruber AR, Bernhart SH, Hofacker IL, Washietl S., BMC Bioinformatics 9(), 2008
PMID: 18302738
Computational prediction of RNA structural motifs involved in posttranscriptional regulatory processes.
Rabani M, Kertesz M, Segal E., Proc Natl Acad Sci U S A 105(39), 2008
PMID: 18815376
RNAalifold: improved consensus structure prediction for RNA alignments.
Bernhart SH, Hofacker IL, Will S, Gruber AR, Stadler PF., BMC Bioinformatics 9(), 2008
PMID: 19014431
RNA localization signals: deciphering the message with bioinformatics.
Hamilton RS, Davis I., Semin Cell Dev Biol 18(2), 2007
PMID: 17452113
RNA stem-loops: to be or not to be cleaved by RNAse III.
Ritchie W, Legendre M, Gautheret D., RNA 13(4), 2007
PMID: 17299129
A structure-based flexible search method for motifs in RNA.
Veksler-Lublinsky I, Ziv-Ukelson M, Barash D, Kedem K., J Comput Biol 14(7), 2007
PMID: 17803370
XML schemas for common bioinformatic data types and their application in workflow systems.
Seibel PN, Krüger J, Hartmeier S, Schwarzer K, Löwenthal K, Mersch H, Dandekar T, Giegerich R., BMC Bioinformatics 7(), 2006
PMID: 17087823
Evolutionary patterns of non-coding RNAs.
Bompfünewerer AF, Flamm C, Fried C, Fritzsch G, Hofacker IL, Lehmann J, Missal K, Mosig A, Müller B, Prohaska SJ, Stadler BM, Stadler PF, Tanzer A, Washietl S, Witwer C., Theory Biosci 123(4), 2005
PMID: 18202870


Markieren/ Markierung löschen
Markierte Publikationen

Open Data PUB


PMID: 16452790
PubMed | Europe PMC

Suchen in

Google Scholar