8 Introduction
Chapter 1 Background – RNAs, non-coding RNAs, and bioinformatics This Chapter presents the background of my thesis, first on biology, then on bioinformatics. In Section 1.1, I present some biological facts on RNAs and non-coding RNAs (ncRNAs). This is not a <strong>de</strong>ep presentation of ncRNAs, but rather an introduction for computer scientists to un<strong>de</strong>rstand why RNA structure is worth of study. Then, in Section 1.2, I present a survey of bioinformatics for RNA <strong>structures</strong>. Finally, Section 1.3 <strong>de</strong>tails the contents of the thesis. 1.1 Ribonucleic acids (RNAs) 1.1.1 RNA and its <strong>structures</strong> The ribonucleic acid (RNA) is a single-stran<strong>de</strong>d molecule composed of a ribose-phosphate backbone carrying a sequence of bases A (A<strong>de</strong>nine), C (Cytosine), G (Guanine), and U (Uracile). Usual RNAs range from about ten to thousands of bases. This sequence, or “primary structure”, is produced by the transcription of genome (see below). The RNA molecule folds upon itself to form base pairs. These pairings are done by hydrogen bonds b<strong>et</strong>ween two nucleic acids. The most common base pairs are Watson-Crick base pairs, or “canonical base pairs”, A–U and C–G. Other combinations are possible, such as the wobble pair G–U. The “secondary structure” of the RNA is a s<strong>et</strong> of non-crossing base pairs (Figure 1.1), creating stems-loops, helices, <strong>multi</strong>-loops and other structural elements (Figure 1.2). In further foldings, some other pairings take place, such as pseudo-knots, for example kissing hairpins, that have crossing base pairs, or even including other bonds such as base tripl<strong>et</strong>s. Of course, the RNA molecule finally folds in the 3D space of the cell, and can interact insi<strong>de</strong> a larger complex, with other RNAs, proteins, or other molecules. 1.1.2 The central dogma and messenger RNA (mRNA) The “central dogma of molecular biology” is <strong>de</strong>picted on the upper part of Figure 1.4 : DNA is replicated, DNA makes RNA trough transcription, and RNA makes proteins through translation. The first i<strong>de</strong>as on this flow of information dates from more than sixty years ago, with papers 9
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Chapter 4 Alterna - Alternate RNA s
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4.1. Multi-structure matching 61 he
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4.1. Multi-structure matching 63 (a
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4.1. Multi-structure matching 65 Se
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4.2. Algorithm 67 T (h, k, ℓ) = m
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4.2. Algorithm 69 4.2 Algorithm We
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4.2. Algorithm 71 used for distinct
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4.3. Adding positional constraints
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4.5. Experimentations 75 sequence f
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4.6. Conclusions 77 Distribution of
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Chapter 5 Conclusion Predicting and
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Bibliography [1] C. Alkan, E. Karak
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[30] S. R. Eddy. How do RNA folding
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[63] K. Lagesen, P. Hallin, E. A. R
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[95] R. Salari, M. Mohl, S. Will, S
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[128] A. Xayaphoummine, T. Bucher,