The software is designed to predict how RNA will fold based on thermodynamic principles, matching complementary sequences to create stable structures. By analyzing the potential energy of different configurations, the program can identify the most likely folding patterns, providing insight into RNA structure and function.
If you're looking for an easy-to-use command-line based tool for folding RNA secondary structures, pknotsRG is worth considering. This free tool includes the class of simple recursive pseudoknots, making it a versatile option for researchers and scientists.
The energy parameters for structures without pseudoknots are identical to those found in mfold 3.1. However, the energy for pseudoknots is computed differently, using a model similar to the one found in pknots by Rivas&Eddy. Additionally, the folding temperature is fixed at 37C for convenience.
Currently, there are three different modes available within pknotsRG. The first, pknotsRG-mfe, computes the minimum free energy structure of s, whether or not it contains pseudoknots. Alternatively, pknotsRG-enf enforces a pseudoknot and delivers the energetically optimal complete structure of s that includes at least one pseudoknot anywhere. Finally, pknotsRG-loc delivers the best local pseudoknot, as defined by free energy per nucleotide. The rest of s remains unfolded.
Overall, pknotsRG is a useful tool for those working with RNA secondary structures, especially those that contain pseudoknots. While it is a command-line based tool, the straightforward modes and free availability make it accessible for users of all levels.
The energy parameters for structures without pseudoknots are identical to those found in mfold 3.1. However, the energy for pseudoknots is computed differently, using a model similar to the one found in pknots by Rivas&Eddy. Additionally, the folding temperature is fixed at 37C for convenience.
Currently, there are three different modes available within pknotsRG. The first, pknotsRG-mfe, computes the minimum free energy structure of s, whether or not it contains pseudoknots. Alternatively, pknotsRG-enf enforces a pseudoknot and delivers the energetically optimal complete structure of s that includes at least one pseudoknot anywhere. Finally, pknotsRG-loc delivers the best local pseudoknot, as defined by free energy per nucleotide. The rest of s remains unfolded.
Overall, pknotsRG is a useful tool for those working with RNA secondary structures, especially those that contain pseudoknots. While it is a command-line based tool, the straightforward modes and free availability make it accessible for users of all levels.
What's New
Version 1.3: N/A