goal

• time-efficient computation of base pair probabilites based on seed-extension predictor strategies

preliminaries

• preliminary formalisms, ideas and method descriptions are provided in
  • https://github.com/BackofenLab/IntaRNA-probabilities/blob/issue-10-fixed-seed-recursions
    • i.e. in branch "issue-10-fixed-seed-recursions" of the "IntaRNA-probabilities" repository
• estimate whether the last formalism for stack-only seeds is faster and easier to integrate into the IntaRNA framework or the automaton-based general approach

task

• formulate a stepwise implementation plan with all details needed for a subsequent implementation (do not implement yet)
  • to revise the seed-extension-based partition function computation to prepare the base pair probability computation
  • to implement efficient base pair probability computation under the assumption of stack-only seeds (to this end, also extend the SeedHandler with a respective check method) unless you are planning to integrate the automaton-based general approach
  • to integrate the base pair probability computation into the existing framework for their output. adapt if necessary