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## Authors ’ Preprint version. The final version is published in:

### Citations

795 | Fast Folding and Comparison of RNA Secondary Structures. Monatshefte fur Chemie
- Hofacker, Fontana, et al.
- 1994
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Citation Context .... The helices can also be computed directly by the server from the RNA sequence. The output is the set of all locally optimal structures, sorted according to the free energy as computed with rnaeval (=-=Hofacker et al., 1994-=-). We also produce an energy landscape graph, useful for visualizing at a glance all found structures. Running times. We show on Table 1 the running times of regliss for a selection of RNA sequences. ... |

649 | Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information - Zuker, Stiegler - 1981 |

426 | The equilibrium partition function and base pair binding probabilities for RNA secondary structure. Biopolymers - McCaskill - 1990 |

382 |
On Finding All Suboptimal Foldings of an RNA Molecule
- Zuker
- 1989
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Citation Context ...RNA sequences which not only have low folding energy, but whose folding landscape would suggest rapid and robust folding. Several programs produce suboptimal foldings of RNA, including mfold/unafold (=-=Zuker, 1989-=-), RNAsubopt (Wuchty et al., 1999) and RNAshapes (Steffen et al., 2006). ∗Corresponding author: helene.touzet@lifl.fr 1 ha l-0 07 56 24 9,sv er sio ns1s- 2 2sNo vs20 12 Author manuscript, published in... |

219 |
RNA secondary structures and their prediction
- Zuker, Sankoff
- 1984
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Citation Context ...se it is the optimal structure containing base pair (33, 75). ima in the free energy landscape. The notions of saturated structures and locally optimal secondary structures meet this requirement. In (=-=Zuker & Sankoff, 1984-=-) and (Evers & Giegerich, 2001), a secondary structure is saturated when the stacking regions are extended maximally in both directions: No base pairs can be added at the extremity of a stacking regio... |

214 | Complete suboptimal folding of RNA and the stability of secondary structures
- Wuchty, Fontana, et al.
- 1999
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Citation Context ...nly have low folding energy, but whose folding landscape would suggest rapid and robust folding. Several programs produce suboptimal foldings of RNA, including mfold/unafold (Zuker, 1989), RNAsubopt (=-=Wuchty et al., 1999-=-) and RNAshapes (Steffen et al., 2006). ∗Corresponding author: helene.touzet@lifl.fr 1 ha l-0 07 56 24 9,sv er sio ns1s- 2 2sNo vs20 12 Author manuscript, published in "Journal of Computational Biolog... |

210 | Algorithms for loop matching. - Nussinov, Piecznik, et al. - 1978 |

196 | On cliques in graphs - Moon, Moser - 1965 |

161 |
Fast algorithm for predicting the secondary structure of single-stranded RNA
- Nussinov, Jacboson
- 1980
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Citation Context ...luded in a locally optimal secondary structure. Clote proposed a dynamic programming algorithm to enumerate such structures. One drawback of this approach is that it uses the Nussinov-Jacobson model (=-=Nussinov & Jacobson, 1980-=-), which does not produce realistic secondary structures. The problem of locally optimal secondary structures with an accurate folding model has been recently addressed in (Lorenz & Clote, 2011). The ... |

97 | UNAFold: software for nucleic acid folding and hybridization - Markham, Zuker |

93 |
Rfam: updates to the RNA families database.
- PP, Daub, et al.
- 2009
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Citation Context ... UGA stop codons as selenocysteines. They are around 60 nucleotides in length and adopt a stem-loop structure. Here we work with sequence Y11109.1/1272-1330, from Oreochromis niloticus (RFAM RF00031 (=-=Gardner et al., 2009-=-)). We first ran unafold asking “all” suboptimal structures (100% suboptimality, option -P 100). This gives 30 structures, displayed in Figure 6. The expected consensus secondary structure is not pres... |

88 |
RNAshapes: an integrated RNA analysis package based on abstract shapes
- Steffen, Voss, et al.
(Show Context)
Citation Context ...se folding landscape would suggest rapid and robust folding. Several programs produce suboptimal foldings of RNA, including mfold/unafold (Zuker, 1989), RNAsubopt (Wuchty et al., 1999) and RNAshapes (=-=Steffen et al., 2006-=-). ∗Corresponding author: helene.touzet@lifl.fr 1 ha l-0 07 56 24 9,sv er sio ns1s- 2 2sNo vs20 12 Author manuscript, published in "Journal of Computational Biology 19, 10 (2012) 1120-1133"sDOI : 10.1... |

51 |
A novel RNA structural motif in the selenocysteine insertion element of eukaryotic selenoprotein mRNAs.
- Walczak, Westhof, et al.
- 1996
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Citation Context ...elices, regliss can be longer for some sequences. 5 Experimentations 5.1 Example on a SECIS element SECIS elements (selenocysteine insertion sequence) occur in messenger RNAs encoding selenoproteins (=-=Walczak et al., 1996-=-) and direct the cell machinery to translate UGA stop codons as selenocysteines. They are around 60 nucleotides in length and adopt a stem-loop structure. Here we work with sequence Y11109.1/1272-1330... |

49 |
Significance of nucleotide sequence alignments: A method for random sequence permutation that preserves dinucleotide and codon usage
- Altschul, Erikson
- 1985
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Citation Context ... sequences with the same length and the same dinucleotide composition. This computation has been performed with the dishuffle program1 that implements the dinucleotide shuffle algorithm described in (=-=Altschul & Erickson, 1985-=-). We then compared the distributions of locally optimal secondary structures between these randomized sequences and the initial sequence. Result is shown on Figure 8. Graphs obtained with regliss are... |

36 |
Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure
- Matthews, Sabina, et al.
- 1999
(Show Context)
Citation Context ...elices. This model is likely to produce more biologically realistic structures, because it takes into account the stacking energy between base pairs, such as introduced in the Nearest Neighbor model (=-=Matthews et al., 1999-=-) for example. 3.2.1 Definitions We admit a generic definition for helices. It is an ordered set of base pairs {(x1, y1), . . . , (xk, yk)} such that x1 < . . . < xk, and y1 > . . . > yk. It can conta... |

26 |
How do RNA folding algorithms work
- Eddy
- 2004
(Show Context)
Citation Context ...ing. Knowing the secondary structures is thus of critical importance to understand the function of an RNA molecule. The earliest algorithms for the RNA folding problem appeared in the late 70’s, see (=-=Eddy, 2004-=-) for a survey. Such algorithms take as input a single stranded RNA sequence and output a single secondary structure possessing minimum free energy. However, it became clear early on that computing th... |

20 | An efficient algorithm to compute the landscape of locally optimal RNA secondary structures with respect to the Nussinov-Jacobson energy model - Clote |

15 | Evaluating the predictability of conformational switching in RNA - Voss - 2004 |

9 | Computing the partition function for kinetically trapped RNA secondary structures
- Lorenz, Clote
- 2011
(Show Context)
Citation Context ... (Nussinov & Jacobson, 1980), which does not produce realistic secondary structures. The problem of locally optimal secondary structures with an accurate folding model has been recently addressed in (=-=Lorenz & Clote, 2011-=-). The authors present an algorithm to compute the partition function over all locally optimal secondary structures of a given RNA sequence, extending the McCaskill’s classical algorithm (J., 1990). T... |

6 | RNALOSS: a web server for RNA locally optimal secondary structures - Clote - 2005 |

2 |
Reducing the Conformation Space
- Evers, Giegerich
- 2001
(Show Context)
Citation Context ...re containing base pair (33, 75). ima in the free energy landscape. The notions of saturated structures and locally optimal secondary structures meet this requirement. In (Zuker & Sankoff, 1984) and (=-=Evers & Giegerich, 2001-=-), a secondary structure is saturated when the stacking regions are extended maximally in both directions: No base pairs can be added at the extremity of a stacking region without degrading the free e... |