KnotAli: informed energy minimization through the use of evolutionary information.

ABSTRACT:

Background

Improving the prediction of structures, especially those containing pseudoknots (structures with crossing base pairs) is an ongoing challenge. Homology-based methods utilize structural similarities within a family to predict the structure. However, their prediction is limited to the consensus structure, and by the quality of the alignment. Minimum free energy (MFE) based methods, on the other hand, do not rely on familial information and can predict structures of novel RNA molecules. Their prediction normally suffers from inaccuracies due to their underlying energy parameters.

Results

We present a new method for prediction of RNA pseudoknotted secondary structures that combines the strengths of MFE prediction and alignment-based methods. KnotAli takes a multiple R

SUBMITTER: Gray M 

PROVIDER: S-EPMC9063079 | biostudies-literature | 2022 May

REPOSITORIES: biostudies-literature