@@ -43,7 +43,11 @@ OBJECTIVE FUNCTIONS FOR THE MODULE INSERTION CRITERIA
***Function C** : weights a module by its insertion site score (JAR3D or BayesPairing score).
***Function D** : weights a module by its number of components (strands) and insertion site score (JAR3D or BayesPairing score), and penalizes it by the log^(_2) of its nucleotide size.
3/ Recommended uses
3/ Installation
==================================
Check the file INSTALL.md for installation instructions.
4/ Recommended uses
==================================
- If **you know you have no pseudoknot**:
* Benchmarks show Biorseo does not perform better than simpler tools like RNAsubopt alone. Please use RNAsubopt (ViennaRNA package) or Fold (RNAstructure package).
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@@ -55,11 +59,6 @@ OBJECTIVE FUNCTIONS FOR THE MODULE INSERTION CRITERIA
* The use of the RNA 3D Motif Atlas placed by JAR3D and scored with function B is not subject to combinatorial issues, but performs a bit worse. It also returns less solutions. Example: