Nucleic Acids Research, Vol 27, Issue 21 4208-4217, Copyright © 1999 by Oxford University Press
R Luck, S Graf and G Steger
A tool for prediction of conserved secondary structure of a set of
homologous single-stranded RNAs is presented. For each RNA of the set the
structure distribution is calculated and stored in a base pair probability
matrix. Gaps, resulting from a multiple sequence alignment of the RNA set,
are introduced into the individual probability matrices. These 'aligned'
probability matrices are summed up to give a consensus probability matrix
emphasizing the conserved structural elements of the RNA set. Because the
multiple sequence alignment is independent of any structural constraints,
such an alignment may result in introduction of gaps into the homologous
probability matrices that disrupt a common consensus structure. By use of
its graphical user interface the presented tool allows the removal of such
misalignments, which are easily recognized, from the individual probability
matrices by optimizing the sequence alignment with respect to a structural
alignment. From the consensus probability matrix a consensus structure is
extracted, which is viewable in three different graphical representations.
The functionality of the tool is demonstrated using a small set of U7 RNAs,
which are involved in 3'-end processing of histone mRNA precursors.
Supplementary Material lists further results obtained. Advantages and
drawbacks of the tool are discussed in comparison to several other
algorithms.
ARTICLES
ConStruct: a tool for thermodynamic controlled prediction of conserved secondary structure
Institut fur Physikalische Biologie, Geb. 26.12.U1, Heinrich-Heine- Universitat Dusseldorf, Universitatsstrasse 1, D-40225 Dusseldorf, Germany.
CiteULike 
Connotea 
Del.icio.us What's this?
This article has been cited by other articles:
|
|
 |
|
  J. Matousek, L. Orctova, J. Ptacek, J. Patzak, P. Dedic, G. Steger, and D. Riesner Experimental Transmission of Pospiviroid Populations to Weed Species Characteristic of Potato and Hop Fields J. Virol., November 1, 2007; 81(21): 11891 - 11899. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 A. Jambhekar and J. L. DeRisi Cis-acting determinants of asymmetric, cytoplasmic RNA transport RNA, May 1, 2007; 13(5): 625 - 642. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 H. Kiryu, T. Kin, and K. Asai Robust prediction of consensus secondary structures using averaged base pairing probability matrices Bioinformatics, February 15, 2007; 23(4): 434 - 441. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. Lindgreen, P. P. Gardner, and A. Krogh Measuring covariation in RNA alignments: physical realism improves information measures Bioinformatics, December 15, 2006; 22(24): 2988 - 2995. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 B. Voss Structural analysis of aligned RNAs Nucleic Acids Res., November 14, 2006; 34(19): 5471 - 5481. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. Marszalkowski, J.-H. Teune, G. Steger, R. K. Hartmann, and D. K. Willkomm Thermostable RNase P RNAs lacking P18 identified in the Aquificales RNA, November 1, 2006; 12(11): 1915 - 1921. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
D. Dalli, A. Wilm, I. Mainz, and G. Steger STRAL: progressive alignment of non-coding RNA using base pairing probability vectors in quadratic time Bioinformatics, July 1, 2006; 22(13): 1593 - 1599. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
T. Gesell and A. von Haeseler In silico sequence evolution with site-specific interactions along phylogenetic trees Bioinformatics, March 15, 2006; 22(6): 716 - 722. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. Siebert and R. Backofen MARNA: multiple alignment and consensus structure prediction of RNAs based on sequence structure comparisons Bioinformatics, August 15, 2005; 21(16): 3352 - 3359. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 R. A. Owens and S. M. Thompson Mutational analysis does not support the existence of a putative tertiary structural element in the left terminal domain of Potato spindle tuber viroid J. Gen. Virol., June 1, 2005; 86(6): 1835 - 1839. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
D. H. Mathews Predicting a set of minimal free energy RNA secondary structures common to two sequences Bioinformatics, May 15, 2005; 21(10): 2246 - 2253. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
R. KNIGHT, A. BIRMINGHAM, and M. YARUS BayesFold: Rational 2{degrees} folds that combine thermodynamic, covariation, and chemical data for aligned RNA sequences RNA, September 1, 2004; 10(9): 1323 - 1336. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. Ruan, G. D. Stormo, and W. Zhang ILM: a web server for predicting RNA secondary structures with pseudoknots Nucleic Acids Res., July 1, 2004; 32(suppl_2): W146 - W149. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
C. Thurner, C. Witwer, I. L. Hofacker, and P. F. Stadler Conserved RNA secondary structures in Flaviviridae genomes J. Gen. Virol., May 1, 2004; 85(5): 1113 - 1124. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 S. L. Chen and L. Shapiro Identification of Long Intergenic Repeat Sequences Associated with DNA Methylation Sites in Caulobacter crescentus and Other {alpha}-Proteobacteria J. Bacteriol., August 15, 2003; 185(16): 4997 - 5002. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
B. Knudsen and J. Hein Pfold: RNA secondary structure prediction using stochastic context-free grammars Nucleic Acids Res., July 1, 2003; 31(13): 3423 - 3428. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
I. L. Hofacker Vienna RNA secondary structure server Nucleic Acids Res., July 1, 2003; 31(13): 3429 - 3431. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
R. A. Owens, S. M. Thompson, and M. Kramer Identification of neutral mutants surrounding two naturally occurring variants of Potato spindle tuber viroid J. Gen. Virol., March 1, 2003; 84(3): 751 - 756. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
C. Witwer, S. Rauscher, I. L. Hofacker, and P. F. Stadler Conserved RNA secondary structures in Picornaviridae genomes Nucleic Acids Res., December 15, 2001; 29(24): 5079 - 5089. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. Graf, D. Strothmann, S. Kurtz, and G. Steger HyPaLib: a database of RNAs and RNA structural elements defined by hybrid patterns Nucleic Acids Res., January 1, 2001; 29(1): 196 - 198. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
R. D. M. Page Comparative analysis of secondary structure of insect mitochondrial small subunit ribosomal RNA using maximum weighted matching Nucleic Acids Res., October 15, 2000; 28(20): 3839 - 3845. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. Antal, A. Mougin, M. Kis, E. Boros, G. Steger, G. Jakab, F. Solymosy, and C. Branlant Molecular characterization at the RNA and gene levels of U3 snoRNA from a unicellular green alga, Chlamydomonas reinhardtii Nucleic Acids Res., August 1, 2000; 28(15): 2959 - 2968. [Abstract] [Full Text] [PDF]
|
|