Fast and accurate structural RNA alignment by progressive lagrangian optimization

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

Volumn 3695 LNBI, Issue , 2005, Pages 217-228

  Bauer, Markus ^a,b   Klau, Gunnar W ^a   Reinert, Knut ^a  

^a FREIE UNIVERSITÄT BERLIN   (Germany)

^b INTERNATIONAL MAX PLANCK RESEARCH SCHOOL FOR COMPUTATIONAL BIOLOGY AND SCIENTIFIC COMPUTING   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHMS; ALIGNMENT; LAGRANGE MULTIPLIERS; LINEAR PROGRAMMING; MOLECULAR STRUCTURE; OPTIMIZATION; PROTEINS;

INTEGER LINEAR PROGRAMMING; LAGRANGIAN OPTIMIZATION; RNA ALIGNMENT; STRUCTURAL ALIGNMENT ALGORITHMS;

RNA;

EID: 33646182212     PISSN: 03029743     EISSN: 16113349     Source Type: Book Series    
DOI: 10.1007/11560500_20     Document Type: Conference Paper

References (27)

1. Hofacker, I.L., Bernhart, S.H.F., Stadler, P.F.: Alignment of RNA base pairing probability matrices. Bioinformatics 20 (2004) 2222-2227
2. Washietl, S., Hofacker, I.L.: Consensus folding of aligned sequences as a new measure for the detection of functional RNAs by comparative genomics. J. Mol. Biol. 342 (2004) 19-30
3. Gardner, P., Wilm, A., Washietl, S.: A benchmark of multiple sequence alignment programs upon structural RNAs. Nucl. Acids Res. 33 (2005) 2433-2439
4. Sankoff, D.: Simultaneous solution of the RNA folding, alignment, and proto-sequence problems. SIAM J. Appl. Math. 45 (1985) 810-825
5. Corpet, F., Michot, B.: RNAlign program: alignment of RNA sequences using both primary and secondary structures. CABIOS 10 (1994) 389-399
6. Mathews, D.H., Turner, D.H.: Dynalign: An algorithm for finding secondary structures common to two RNA sequences. J. Mol. Biol. 317 (2002) 191-203
7. Mathews, D.: Predicting a set of minimal free energy RNA secondary structures common to two sequences. Bioinformatics 21 (2005) 2246-2253
8. Gorodkin, J., Heyer, L.J., Stormo, G.D.: Finding the most significant common sequence and structure motifs in a set of RNA sequences. Nucl. Acids Res. 25 (1997) 3724-3732
9. Hull Havgaard, J., Lyngsø, R., Stormo, G., Gorodkin, J.: Pairwise local structural alignment of RNA sequences with sequence similarity less than 40%. Bioinformatics 21 (2005) 1815-1824
10. Holmes, I.: A probabilistic model for the evolution of RNA structure. BMC Bioinformatics 5 (2004) 166
11. Holmes, I.: Accelerated probabilistic inference of RNA structure evolution. BMC Bioinformatics 5 (2004) 73
12. Bafna, V., Muthukrishnan, S., Ravi, R.: Computing similarity between RNA strings. In: Proc. of CPM'95. Number 937 in LNCS, Springer (1995) 1-16
13. Waterman, M.S.: Consensus methods for folding single-stranded nucleic adds. Mathematical Methods for DNA Sequences (1989) 185-224
14. Eddy, S.P., Durbin, R.: RNA sequence analysis using covariance models. Nucl. Acids Research 22 (1994) 2079-2088
15. McCaskill, J.S.: The Equilibrium Partition Function and Base Pair Binding Probabilities for RNA Secondary Structure. Biopolymers 29 (1990) 1105-1119
16. Lenhof, H.P., Reinert, K., Vingron, M.: A polyhedral approach to RNA sequence structure alignment. Journal of Comp. Biology 5 (1998) 517-530
17. Caprara, A., Lancia, G.: Structural alignment of large-size proteins via Lagrangian relaxation. In: Proc. of RECOMB'02, ACM Press (2002) 100-108
18. Bauer, M., Klau, G.W.: Structural alignment of two RNA sequences with La-grangian relaxation. In: Proc. of ISAAC'04. Number 3341 in LNCS, Springer (2004) 113-123
19. Bauer, M., Klau, G.W., Reinert, K.: Multiple structural RNA alignment with Lagrangian relaxation. In: Proc. of WABI 2005. LNBI (2005) To appear.
20. Notredame, C., Higgins, D.G., Heringa, J.: T-Coffee: A novel method for fast and accurate multiple sequence alignment. Journal of Molecular Biology (2000)
21. Thompson, J.D., Higgins, D.G., Gibson, T.J.: Clustal w: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, positions-specific gap penalties and weight matrix choice. Nucl. Acids Res. 22 (1994) 4673-4680
22. Siebert, S., Backofen, R.: MARNA: Multiple alignment and consensus structure prediction of RNAs based on sequence structure comparisons. Bioinformatics (2005) In press.
23. Jiang, T., Lin, G.H., Ma, B., Zhang, K.: A general edit distance between RNA structures. J. of Computational Biology 9 (2002) 371-388
24. Gotoh, O.: An improved algorithm for matching biological sequences. Journal of Molecular Biology (1982) 705-708
25. Kececioglu, J., Lenhof, H.P., Mehlhorn, K., Mutzel, P., Reinert, K., Vingron, M.: A polyhedral approach to sequence alignment problems. Discrete Applied Mathematics 104 (2000) 143-186
26. Huang, X., Miller, W.: A time efficient, linear space local similarity algorithm. Adv. Appl. Math. 12 (1991) 337-357
27. Dirks, R., Pierce, N.: An algorithm for computing nucleic acid base-pairing probabilities including pseudoknots. Journal of Computational Chemistry 25 (2004) 1295-1304