Abstract
Dynamic programming algorithms solve many standard problems of RNA bioinformatics in polynomial time. In this contribution we discuss a series of variations on these standard methods that implement refined biophysical models, such as a restriction of RNA folding to canonical structures, and an extension of structural alignments to an explicit scoring of stacking propensities. Furthermore, we demonstrate that a local structural alignment can be employed for ncRNA gene finding. In this context we discuss scanning variants for folding and alignment algorithms.
Article PDF
Similar content being viewed by others
Avoid common mistakes on your manuscript.
References
Backofen R. and Will S. (2004). Local sequence–structure motifs in RNA. J. Bioinform. Comput. Biol. 2: 681–698
Bernhart S., Hofacker I.L. and Stadler P.F. (2006). Local RNA base pairing probabilities in large sequences. Bioinformatics 22: 614–615
Deng W., Zhu X., Skogerbø G., Zhao Y., Fu Z., Wang Y., He Housheng Cai L., Sun H., Liu C., Li B.L., Bai B., Wang J., Cui Y., Jai D., Wang Y., Du D. and Chen R. (2006). Organisation of the Caenorhabditis elegans small noncoding transiptome: genomic features, biogenesis and expression. Genome Res. 16: 30–36
Ding, Y., Chan, C.Y., Lawrence, C.E.: Sfold web server for statistical folding and rational design of nucleic acids. Nucleic Acids Res. 32(Web Server issue), W135–W141 (2004)
Doench J.G. and Sharp P.A. (2004). of mioRNA target selection in translational repression. Genes Dev. 18: 504–511
Dulucq S. and Tichit L. (2003). Secondary structure comparison: exact analysis of the Zhang-Shasha tree-edit algorithm. Theor. Comput. Sci. 306: 471–484
Hofacker I.L. (2003). Vienna RNA secondary structure server. Nucleic Acids Res. 31: 3429–3431
Hofacker I.L., Bernhart S.H.F. and Stadler P.F. (2004). Alignment of RNA base pairing probability matrices. Bioinformatics 20: 2222–2227
Hofacker I.L., Fontana W., Stadler P.F., Bonhoeffer S., Tacker M. and Schuster P. (1994). Fast folding and comparison of RNA secondary structures. Monatsh. Chem. 125(2): 167–188
Hofacker I.L., Priwitzer B. and Stadler P.F. (2004). Prediction of locally stable RNA secondary structures for genome-wide surveys. Bioinformatics 20: 191–198
Jiang T., Lin G., Ma B. and Zhang K. (2002). A general edit distance between RNA structures. J. Comput. Biol. 9: 371–88
Klein R.J. and Eddy S.R. (2003). RSEARCH: finding homologs of single structured RNA sequences. BMC Bioinform 4(1): 44
Leydold, J., Stadler, P.F.: Minimal cycle basis of outerplanar graphs. Elec. J. Comb. 5, 209–222 [R16: 14 p.] (1998)
Lin, G.H., Ma, B., Zhang, K.: Edit distance between two RNA structures. In: Proceedings of the 5th Annual International Conference on Computational Biology RECOMB01, pp. 211–220. ACM Press (2001)
Lyngsø R.B., Zuker M. and Pedersen C.N. (1999). Fast evaluation of internal loops in RNA secondary structure prediction. Bioinformatics 15: 440–445
Mathews D., Sabina J., Zuker M. and Turner H. (1999). Expanded sequence dependence of thermodynamic parameters provides robust prediction of RNA secondary structure. J. Mol. Biol. 288: 911–940
Mathews D.H., Disney M.D., Childs J.L., Schroeder S.J., Zuker M. and Turner D.H. (2004). Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure. Proc. Natl. Acad. Sci. USA 101: 7287–7292
McCaskill J.S. (1990). The equilibrium partition function and base pair binding probabilities for RNA secondary structure. Biopolymers 29: 1105–1119
Mückstein U., Tafer H., Hackermüller J., Bernhart S., Stadler P.F. and Hofacker I.L. (2006). Thermodynamics of RNA-RNA binding. Bioinformatics 22: 1177–1182
Sankoff D. (1985). Simultaneous solution of the RNA folding, alignment and proto-sequence problems. SIAM J. Appl. Math. 45: 810–825
Shao, Y., Wu, Y., Chan, C.Y., Mcdonough, K., Ding, Y.: Rational design and rapid seening of antisense oligonucleotides for prokaryotic gene modulation. Nucleic Acids Res. 34, 5660–5669 (2006)
Stricklin, S.L., Griffiths-Jones, S., Eddy, S.R.: C. elegans noncoding RNA genes. WormBook doi:10.1895/wormbook.1.7.1. http://www.wormbook.org/chapters/www_noncodingRNA/noncoding RNA.html (2005)
Tinoco I., Uhlenbeck O.C. and Levine M.D. (1971). Estimation of secondary structure in ribonucleic acids. Nature 230: 362–367
Will, S., Reiche, K., Hofacker, I.L., Stadler, P.F., Backofen, R.: Inferring non-coding RNA families and classes by means of genome-scale structure-based clustering. PLoS Comp. Biol. 3, e65 (2007)
Zemann A., op de Bekke A., Kiefmann M., Brosius J. and Schmitz J. (2006). Evolution of small nucleolar RNAs in nematodes. Nucleic Acids Res. 34: 2676–2685
Zuker M. and Sankoff D. (1984). RNA secondary structures and their prediction. Bull. Math. Biol. 46: 591–621
Zuker M. and Stiegler P. (1981). Optimal computer folding of larger RNA sequences using thermodynamics and auxiliary information. Nucleic Acids Res. 9: 133–148
Author information
Authors and Affiliations
Corresponding author
Rights and permissions
About this article
Cite this article
Bompfünewerer, A.F., Backofen, R., Bernhart, S.H. et al. Variations on RNA folding and alignment: lessons from Benasque. J. Math. Biol. 56, 129–144 (2008). https://doi.org/10.1007/s00285-007-0107-5
Received:
Revised:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s00285-007-0107-5