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Pure Multiple RNA Secondary Structure Alignments: A Progressive Profile Approach
January-March 2004 (vol. 1 no. 1)
pp. 53-62
ASCII Text
x 
 
Matthias Höchsmann, Björn Voss, Robert Giegerich, "Pure Multiple RNA Secondary Structure Alignments: A Progressive Profile Approach," IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 1, no. 1, pp. 53-62, January-March, 2004.
 
 
BibTex
x
 
@article{ 10.1109/TCBB.2004.11,
author = {Matthias Höchsmann and Björn Voss and Robert Giegerich},
title = {Pure Multiple RNA Secondary Structure Alignments: A Progressive Profile Approach},
journal ={IEEE/ACM Transactions on Computational Biology and Bioinformatics},
volume = {1},
number = {1},
issn = {1545-5963},
year = {2004},
pages = {53-62},
doi = {http://doi.ieeecomputersociety.org/10.1109/TCBB.2004.11},
publisher = {IEEE Computer Society},
address = {Los Alamitos, CA, USA},
}
 
 
RefWorks Procite/RefMan/Endnote
x 
 
TY - JOUR
JO - IEEE/ACM Transactions on Computational Biology and Bioinformatics
TI - Pure Multiple RNA Secondary Structure Alignments: A Progressive Profile Approach
IS - 1
SN - 1545-5963
SP53
EP62
EPD - 53-62
A1 - Matthias Höchsmann,
A1 - Björn Voss,
A1 - Robert Giegerich,
PY - 2004
KW - Alignment of trees
KW - RNA secondary structures
KW - noncoding RNAs.
VL - 1
JA - IEEE/ACM Transactions on Computational Biology and Bioinformatics
ER -
 
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.

[1] B.A. Shapiro and K. Zhang, Comparing Multiple RNA Secondary Structures Using Tree Comparisons Computer Applications in the Biosciences, vol. 6, no. 4, pp. 309-318, 1990.
[2] F. Corpet and B. Michot, RNAlign Program: Alignment of RNA Sequences Using Both Primary and Secondary Structures Computer Applications in the Biosciences, vol. 10, no. 4, pp. 389-399, 1994.
[3] T. Jiang, G. Lin, B. Ma, and K. Zhang, A General Edit Distance between RNA Structures J. Computational Biology, vol. 9, no. 2, pp. 371-388, 2002.
[4] K. Wojciech and B. Shapiro, Stem Trace: An Interactive Visual Tool for Comparative RNA Structure Analysis. Bioinformatics, vol. 15, no. 1, pp. 16-31, 1999.
[5] B. Shapiro, An Algorithm for Comparing Multiple RNA Secondary Stuctures Computer Applications in the Biosciences, vol. 4, no. 3, pp. 387-393, 1988.
[6] S. Siebert and R. Backofen, MARNA: A Server for Multiple Alignment of Rnas Proc. German Conf. Bioinformatics, pp. 135-140, 2003.
[7] C. Notredame, D. Higgins, and J. Heringa, T-Coffee: A Novel Method for Fast and Accurate Multiple Sequence Alignment J. Molecular Biology, vol. 302, pp. 205-217, 2000.
[8] T. Jiang, J. Wang, and K. Zhang, Alignment of Trees An Alternative to Tree Edit Theoretical Computer Science, vol. 143, no. 1, pp. 137-148, 1995.
[9] J. Thompson, D. Higgins, and T. Gibson, CLUSTAL W: Improving the Sensitivity of Progressive Multiple Sequence Alignment through Sequence Weighting, Position Specific Gap Penalties and Weight Matrix Choice Nucleic Acids Research, vol. 22, pp. 4673-4680, 1994.
[10] D. Feng and F. Doolittle, Progressive Sequence Alignment as a Prerequisite to Correct to Correct Phylogenetic Trees J. Molecular Evolution, vol. 25, pp. 351-360, 1987.
[11] P. Kilpeläinen and H. Mannila, Ordered and Unordered Tree Inclusion SIAM J. Computing, vol. 24, pp. 340-356, 1995.
[12] D. Reis, P. Golgher, A. Silva, and A. Laender, Automatic Web News Extraction Using Tree Edit Distance Proc. 13th Conf. World Wide Web, pp. 502-511, 2004.
[13] B. Rössler, J. Zhang, and M. Höchsmann, Visual Guided Grasping and Generalization Using Self-Valuing Learning Proc. IEEE/RSJ Int'l Conf. Intelligent Robots and Systems, 2002.
[14] T. Sebastian, P. Klein, B. Kimia, Recognition of Shapes by Editing Their Shock Graphs IEEE Trans. Pattern Analysis and Machine Intelligence, vol. 26, pp. 550-571, 2004.
[15] M. Höchsmann, T. Toller, R. Giegerich, and S. Kurtz, Local Similarity in RNA Secondary Structures Proc. IEEE Computational Systems Bioinformatics Conf., pp. 159-168, 2003.
[16] I. Hofacker, W. Fontana, P. Stadler, S. Bonhoeffer, M. Tacker, and P. Schuster, Fast Folding and Comparison of RNA Secondary Structures Monatshefte f. Chemie, vol. 125, pp. 167-188, 1994.
[17] K. Tai, The Tree-to-Tree Correction Problem J. ACM, vol. 26, pp. 422-433, 1979.
[18] L. Wang and T. Jiang, On the Complexity of Multiple Sequence Alignment J. Computational Biology, vol. 1, pp. 337-348, 1994.
[19] P. Bonizzoni and G. Della Vedova, The Complexity of Multiple Sequence Alignment with Sp-Score that is a Metric Theoretical Computer Science, vol. 259, no. 1, pp. 63-79, 2001.
[20] S. Le, R. Nussinov, and J. Mazel, Tree Graphs of RNA Secondary Structures and Their Comparison Computational Biomedical Research, vol. 22, pp. 461-473, 1989.
[21] T. Lowe and S. Eddy, tRNAscan-se: A Program for Improved Detection of Transfer RNA Genes in Genomic Sequence Nucleic Acids Research, vol. 25, pp. 955-964, 1997.
[22] D. Dowell and S. Eddy, Evaluation of Several Lightweight Stochastic Context-Free Grammars for RNA Secondary Structure Prediction BMC Bioinformatics, vol. 5, no. 71, 2004.
[23] M. Gribskov, A. McLachlan, D. Eisenberg, Profile Analysis Detection of Distantly Related Proteins Proc. Nat'l. Academy of Science, no. 88, vol. 43, pp. 55-58, 1987.
[24] H. Carillo and D. Lipman, The Multiple Sequence Alignment Problem in Biology SIAM J. Applied Math., vol. 48, no. 5, pp. 1073-1082, 1988.
[25] M. Zuker and P. Stiegler, Optimal Computer Folding of Large RNA Sequences Using Thermodynamics and Auxiliary Information Nucleic Acids Research, vol. 9, pp. 133-148, 1981.
[26] K. Zhang and D. Shasha, Simple Fast Algorithms for the Editing Distance between Trees and Related Problems SIAM J. Computing, vol. 18, no. 6, pp. 1245-1262, 1989.
[27] P.N. Klein, Computing the Edit-Distance between Unrooted Ordered Trees Proc. Sixth Ann. European Symp., no. 1461, pp. 91-102, 1998.
[28] S. Dulucq and H. Touzet, Analysis of Tree Edit Distance Algorithms Proc. 14th Ann. Symp. Combinatorial Pattern Matching, pp. 83-95, 2003.
[29] S. Dulucq and L. Tichit, RNA Secondary Structure Comparison: Exact Analysis of the Zhang-Sasha Tree Edit-Algorithm Theoretical Computer Science, vol. 306, pp. 471-484, 2003.
[30] D. Konings and P. Hogeweg, Pattern Analysis of RNA Secondary Structure: Similarity and Consensus of Minimal-Energy Folding J. Molecular Biology, vol. 207, pp. 597-614, 1989.
[31] F. Chetouani, P. Monestie, P. Thebault, C. Gaspin, and B. Michot, ESSA: An Integrated and Interactive Computer Tool for Analysing RNA Secondary Structure Nucleic Acids Research, vol. 25, no. 17, pp. 3514-3522, 1997.
[32] G. Pesole, S. Liuni, G. Grillo, F. Licciulli, F. Mignone, C. Gissi, and C. Saccone, Utrdb and Utrsite: Specialized Database of Sequences and Functional Elements of 5' and 3' Untranslated Regions of Eukaryotic mRNAs Nucleic Acids Research, vol. 30, pp. 335-340, 2002.
[33] M. Zuker, Mfold Web Server for Nucleic Acid Folding and Hybridization Prediction Nucleic Acids Research, vol. 31, no. 13, pp. 3406-3415, 2003.
[34] I. Hofacker, Vienna RNA Secondary Structure Server Nucleic Acids Research, vol. 31, no. 13, pp. 3429-3431, 2003.
[35] A. Wong and D. Chiu, An Event-Covering Method for Effective Probabilistic Inference Pattern Recognition, vol. 20, pp. 245-255, 1987.
[36] D. Chiu and T. Kolodziejczak, Inferring Consensus Structure from Nucleic Acid Sequences Computer Applications in the Biosciences, vol. 7, pp. 347-352, 1991.
[37] J. Gorodkin, L. Heyer, S. Brunak, and G. Stormo, Displaying the Information Contents of Structural RNA Alignments Bioinformatics, vol. 13, pp. 583-586, 1997.
[38] M. Mandal, B. Boese, J. Barrick, W. Winkler, and R. Breaker, Riboswitches Control Fundamental Biochemical Pathways in Bacillus Subtilis and Other Bacteria Cell, vol. 113, no. 5, pp. 577-586, 2003.
[39] S. Griffiths-Jones, A. Bateman, M. Marshall, A. Khanna, and S. Eddy, Rfam: An RNA Family Database Nucleic Acids Research, vol. 31, no. 1, pp. 439-441, 2003.
[40] I. Hofacker, M. Fekete, and P. Stadler, Secondary Structure Prediction for Aligned RNA Sequences J. Molecular Biology, vol. 319, pp. 1059-1066, 2002.
[41] K. Zhang, Computing Similarity between RNA Secondary Structures Proc. IEEE Int'l Joint Symp. Intelligence and Systems, pp. 126-132, 1998.

Index Terms:
Alignment of trees, RNA secondary structures, noncoding RNAs.
Citation:
Matthias Höchsmann, Björn Voss, Robert Giegerich, "Pure Multiple RNA Secondary Structure Alignments: A Progressive Profile Approach," IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 1, no. 1, pp. 53-62, Jan.-March 2004, doi:10.1109/TCBB.2004.11
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