From 72312325fbd382b4eb0cbefeac4066b1950ab56e Mon Sep 17 00:00:00 2001 From: H Wayment-Steele Date: Sun, 20 Jun 2021 13:46:59 -0700 Subject: [PATCH] Update README.md --- README.md | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) diff --git a/README.md b/README.md index e2edec3..480a016 100644 --- a/README.md +++ b/README.md @@ -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 |