I am using FARFAR to get the possible structures for a A-bulge RNA duplex with the following specifications:
Input sequence: CCGGCAGUGUG+CACACGUCGG
Input secstruct (((((.(((((+))))))))))
I need to keep the structure in the duplex form and not the hairpin. All output files I got with the mentioned specifications are RNA hairpins. Is there a way I can keep the structure in the duplex form.
thanks for yoyr help.