Variations on RNA Folding and Alignment

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 pr opensities. Furthermore, we demonstrate that a local structural alignment can be employed for ncRNA gene finding. In this context we discuss scanning variants for fol ding and alignment algorithms.

[1]  Peter F. Stadler,et al.  Prediction of locally stable RNA secondary structures for genome-wide surveys , 2004, Bioinform..

[2]  Rolf Backofen,et al.  Inferring Noncoding RNA Families and Classes by Means of Genome-Scale Structure-Based Clustering , 2007, PLoS Comput. Biol..

[3]  Sean R. Eddy,et al.  RSEARCH: Finding homologs of single structured RNA sequences , 2003, BMC Bioinformatics.

[4]  Bin Ma,et al.  A General Edit Distance between RNA Structures , 2002, J. Comput. Biol..

[5]  J. McCaskill.  The equilibrium partition function and base pair binding probabilities for RNA secondary structure , 1990, Biopolymers.

[6]  J. Sabina,et al.  Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure. , 1999, Journal of molecular biology.

[7]  Walter Fontana,et al.  Fast folding and comparison of RNA secondary structures , 1994 .

[8]  Christian N. S. Pedersen,et al.  Fast evaluation of internal loops in RNA secondary structure prediction , 1999, Bioinform..

[9]  Laurent Tichit,et al.  RNA secondary structure comparison: exact analysis of the Zhang-Shasha tree edit algorithm , 2003, Theor. Comput. Sci..

[10]  Ivo L. Hofacker,et al.  Vienna RNA secondary structure server , 2003, Nucleic Acids Res..

[11]  Peter F. Stadler,et al.  Local RNA base pairing probabilities in large sequences , 2006, Bioinform..

[12]  Rolf Backofen,et al.  Local Sequence-structure Motifs in Rna , 2004, J. Bioinform. Comput. Biol..

[13]  I. Tinoco,et al.  Estimation of Secondary Structure in Ribonucleic Acids , 1971, Nature.

[14]  John G Doench,et al.  Specificity of microRNA target selection in translational repression. , 2004, Genes & development.

[15]  Jürgen Brosius,et al.  Evolution of small nucleolar RNAs in nematodes , 2006, Nucleic acids research.

[16]  D. Turner,et al.  Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[17]  Peter F. Stadler,et al.  Thermodynamics of RNA-RNA Binding , 2006, German Conference on Bioinformatics.

[18]  Michael Zuker,et al.  Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information , 1981, Nucleic Acids Res..

[19]  D. Sankoff.  Simultaneous Solution of the RNA Folding, Alignment and Protosequence Problems , 1985 .

[20]  David Sankoff,et al.  RNA secondary structures and their prediction , 1984 .

[21]  Peter F. Stadler,et al.  Alignment of RNA base pairing probability matrices , 2004, Bioinform..