Open
Description
Right now OSTIR will predict the translation initiation rate for a start codon given the surrounding mRNA sequence. It does not have the "reverse" capability of designing (or mutating) a sequence that has a desired translation initiation rate.
I'd propose adding a separate module with a function run_ostir_design() that will output mRNA/RBS sequences that have predicted translation initiation rates in a specified range for a given open-reading frame. It should also probably be implemented as a separate command-line script named ostir-design or similar. There will need to be some way of specifying the constraints on the sequence and/or where mutation of the sequence is allowed.