Abstract

Pseudoknot is an important motif in RNA secondary structure. Early researchers of RNA secondary structure prediction ignored pseudoknots, but now pseudoknot is in focus in RNA secondary structure prediction. Several algorithms like dynamic programming, comparative algorithms, heuristic algorithms, formal grammar algorithms etc have so far been used for pseudoknot prediction, but the prediction of arbitrary pseudoknots is still an open problem. Also, there does not exist standard categorization of pseudoknot types. This article provides a brief description and comparison of various algorithms being used in pseudoknot prediction along with an overview of various forms of pseudoknots and their representations.

Keywords: Comparative algorithm, dynamic programming, formal grammar, heuristics, pseudoknot, RNA secondary structure.