finding terminal closing stem in a sequence

Question

[joshlhj]

Hi everyone,

I am trying to find the best way to identify a terminal closing stem in a sequence. The sequence of interest would typically have unique sequence motifs at 5' and 3' ends respectively.

So,

5' XXXXXXXX[MotifA]...................[MotifB]XXXXXXXXX 3'

Basically, I would like to get the 10nt upstream of Motif A and 10nt downstream of Motif B, and compare them together to find whether they would form a stem structure (complementary).

I was thinking of getting the reverse complement of one subsequence and align it to the other subsequence. I would identify the motif using BBDuck (of BBtools package), and use aligning tools to identify the structure. My question is, is there a faster/easier way to go about this problem?

Many thanks,

Josh

Answer 1

[Devon Ryan]

Have you considered just using RNAfold? It'll find the stem and any other obvious structure and output things in a text format that you can parse (or just look at manually if you just have a single sequence). That's probably simpler than doing things manually.