Detect 3' end of SSU

Question

Detect 3' end of SSU

brendanf opened this issue 4 years ago · 1 comments

This would be helpful for studies using primers that include enough SSU to be useful.

Answer 1 · 2020-06-16T20:26:45.000Z

To detect SSU: There is not a lot of conserved short-range secondary structure at the 3' end of SSU. Either use a CM including all of V10 and the helix it sits on, or HMMs (the same ones used in ITSx?).