NDLI: SARNA-Predict: A Study of RNA Secondary Structure Prediction Using Different Annealing Schedules

Content Provider	IEEE Xplore Digital Library
Author	Tsang, H.H. Wiese, K.C.
Copyright Year	2007
Description	Author affiliation: Sch. of Comput. Sci., Simon Fraser Univ., Surrey, BC (Tsang, H.H.; Wiese, K.C.)
Abstract	This paper presents an algorithm for RNA secondary structure prediction based on simulated annealing (SA) and also studies the effect of using different types of annealing schedules. SA is known to be effective in solving many different types of minimization problems and for being able to approximate global minima in the solution space. Based on free energy minimization techniques, this permutation-based SA algorithm heuristically searches for the structure with a free energy value close to the minimum free energy DeltaG for that strand, within given constraints. Other contributions of this paper include the use of permutation-based encoding for RNA secondary structure and the swap mutation operator. Also, a detailed study of the convergence behavior of the algorithm is conducted and various annealing schedules are investigated. An evaluation of the performance of the new algorithm in terms of prediction accuracy is made via comparison with the dynamic programming algorithm mfold for thirteen individual known structures from four RNA classes (5S rRNA, Group I intron 23 rRNA, Group I intron 16S rRNA and 16S rRNA). Although dynamic programming algorithms for RNA folding are guaranteed to give the mathematically optimal (minimum energy) structure, the fundamental problem of this approach seems to be that the thermodynamic model is only accurate within 5-10%. Therefore, it is difficult for a single sequence folding algorithm to resolve which of the plausible lowest-energy structure is correct. The new algorithm showed comparable results with mfold and demonstrated a slightly higher specificity
Starting Page	239
Ending Page	246
File Size	258115
Page Count	8
File Format	PDF
ISBN	1424407109
DOI	10.1109/CIBCB.2007.4221229
Language	English
Publisher	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Publisher Date	2007-04-01
Publisher Place	USA
Access Restriction	Subscribed
Rights Holder	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Subject Keyword	RNA Heuristic algorithms Scheduling algorithm Simulated annealing Dynamic programming Predictive models Minimization methods Encoding Genetic mutations Convergence
Content Type	Text
Resource Type	Article

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SARNA-Predict: A Simulated Annealing Algorithm for RNA Secondary Structure Prediction

SARNA-Predict: Using adaptive annealing schedule and inversion mutation operator for RNA secondary structure prediction

SARNA-Predict: Accuracy Improvement of RNA Secondary Structure Prediction Using Permutation-Based Simulated Annealing

SARNA-Predict-pk: Predicting RNA secondary structures including pseudoknots

Sarna-predict: a study of rna secondary structure prediction using different annealing schedules (2007).

Sarna-predict: a simulated annealing algorithm for rna secondary structure prediction (2006).

Heuristic Algorithm for Pseudoknotted RNA Structure Prediction

Sarna-predict: a permutation-based simulated annealing algorithm for rna secondary structure prediction

SARNA-ensemble-predict: The effect of different dissimilarity metrics on a novel ensemble-based RNA secondary structure prediction algorithm

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