RNA Secondary Structure Prediction Algorithms
نویسنده
چکیده
RNA secondary structure prediction is an important problem studied extensively in the past three dacades. However, pseudoknots are usually excluded in RNA secondary structure prediction due to the hardness of examining all possible structures efficiently and model the energy correctly. Current algorithms on predicting structures with pseudoknots usually have extremely high resource requirements and hence impratical. In this paper, we use the energy model proposed by Dirk and Pierce [5] and present two algorithms for nucleic acid secondary structure prediction including pseudoknots. Our algorithm for simple pseudoknots only requires O(N) time and O(N) space. We also designed an O(N) algorithm for recursive pseudoknot structures.
منابع مشابه
PreRkTAG: Prediction of RNA Knotted Structures Using Tree Adjoining Grammars
Background: RNA molecules play many important regulatory, catalytic and structural <span style="font-variant: normal; font-style: norma...
متن کاملDP Algorithms for RNA Secondary Structure Prediction with Pseudoknots
This paper describes simple DP (dynamic programming) algorithms for RNA secondary structure prediction with pseudoknots, for which no explicit DP algorithm had been known. Results of preliminary computational experiments are described too.
متن کاملA Progressive Folding Algorithm for RNA Secondary Structure Prediction
RNA secondary structure prediction is an area where computational techniques have shown great promise. Most RNA secondary structure prediction algorithms use dynamic programming to compute a secondary structure with minimum free energy. Energy minimization algorithms are less accurate on larger RNA molecules. One potential reason is that larger RNA molecules do not fold instantaneously. Instead...
متن کاملConsensus Folding of Unaligned RNA Sequences Revisited
As one of the earliest problems in computational biology, RNA secondary structure prediction (sometimes referred to as "RNA folding") problem has attracted attention again, thanks to the recent discoveries of many novel non-coding RNA molecules. The two common approaches to this problem are de novo prediction of RNA secondary structure based on energy minimization and the consensus folding appr...
متن کاملLinear Time Algorithm for Parsing RNA Secondary Structure
Accurate prediction of pseudoknotted RNA secondary structure is an important computational challenge. Typical prediction algorithms aim to find a structure with minimum free energy according to some thermodynamic (“sum of loop energies”) model that is implicit in the recurrences of the algorithm. However, a clear definition of what exactly are the loops and stems in pseudoknotted structures, an...
متن کامل