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Article information
2001 , Volume 6, ¹ 5, p.3-23
Elloumi M.
Algorithms for the prediction of RNA secondary structures
In this paper, we tackle the problem of the prediction by energy computation of RNA stable secondary structures. We present, under the Hypothesis of Loops Dependent Energy (HLDE), our dynamic programming algorithm to compute the free energies of the stable secondary structures and our traceback algorithm to predict these structures. We compute the free energies of the stable secondary structures by using a new approach, called {it m-Multiloop Approach} (-MA), . This computation is achieved within a time proportional to and using a memory space proportional to . The prediction of the stable secondary structures is achieved within a time proportional to . Compared to other approaches, the -MA enables us to improve the estimation of the minimum energetic contributions of the {it multiloops}. And hence, it enables us to improve the estimation of the free energies of the stable secondary structures.
[full text] Classificator Msc2000:- *90C30 Nonlinear programming
- 90C39 Dynamic programming
- 92C40 Biochemistry, molecular biology
Keywords: RNA secondary structure, prediction, m-multiloop approach
Author(s):
Elloumi M
Office: Computer Science Department, Faculty of Economic Sciences and Management of Tunis, Tunisia
Address: Tunisia, Tunis
E-mail: Mourad.Elloumi@fsegt.rnu.tn
Bibliography link:
Elloumi M. Algorithms for the prediction of RNA secondary structures // Computational technologies. 2001. V. 6. ¹ 5. P. 3-23
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