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Update README.md
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HWaymentSteele authored Jun 20, 2021
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Expand Up @@ -120,15 +120,15 @@ This code has been modified in two ways that means its output, even using the CO

2. The minimum allowable hairpin size was increased from `0` to `3` to prevent structure predictions with `(())` hairpins. To revert back to the original CONTRAfold behavior, set `C_MIN_HP_LENGTH=0` in `Config.hpp` before compiling.

Example Hammerhead Ribozyme sequence: `CGCUGUCUGUACUUGUAUCAGUACACUGACGAGUCCCUAAAGGACGAAACAGCG`
Predictions for Hammerhead Ribozyme sequence, using default CONTRAfold parameters: `CGCUGUCUGUACUUGUAUCAGUACACUGACGAGUCCCUAAAGGACGAAACAGCG`

contrafold predict hhr.bpseq
contrafold predict hhr.bpseq --partition


CONTRAfold v2.02:
CONTRAfold-SE:
EternaFold code, C_MIN_HP_LENGTH=0:
EternaFold code, C_MIN_HP_LENGTH=3:
|CONTRAfold v2.02| 6.87394|
|CONTRAfold-SE| 6.87394|
|EternaFold code, no ML fix and C_MIN_HP_LENGTH=0| 6.87394|
|EternaFold code, C_MIN_HP_LENGTH=0| 6.83585|
|EternaFold code | 6.77285 |



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