iGEM has a collection of many ribosomal binding sites (RBS) at varying strength. eg, BBa_B0030, B0031, B0032, and BBa-J61100-J61150. On the other hand, RBS calculator ( https://salislab.net/software/ ) offers flexibility to design and predict RBS strength. Which tool predicts RBS more accurately? How well are the results from the two correlated? Does anyone have any experience in comparing these two?
My personal experience is that RBSs from iGEM collection are more arbitrary. The translation level depends on the genetic context and coding sequences. The RBS calculator taking those things into account, which might be more accurate in predicting translation level.
I would highly recommend the RBS Calculator. Exactly for the reason you mention: context. It's not extremely accurate, but it's the best out there for now. We use this calculator a lot in our lab. In my experience, it's quite good as long as you don't go to the extremes, like RBSs predicted to have TIRs higher than 100'000 or extremely low. This scale is however anyway relative. So you will also get different outcomes depending on promoter, backbone, strain, etc. However, for several RBSs with different TIRs in the same context correlate quite okay with the prediction.
I also agreed with Yijie and Daniel that RBS calculator is a great tool for prediction with good result, at least for what we have done in Zymomonas mobilis, which has a good correlation between the predicted RBS strengths and experimental results using dual-reporter gene FACS system, detials in our paper "
Prediction and characterization of promoters and ribosomal binding sites of Zymomonas mobilis in system biology era" : https://biotechnologyforbiofuels.biomedcentral.com/articles/10.1186/s13068-019-1399-6
I also agreed with Yijie and Daniel that RBS calculator is a great tool for prediction with good result, at least for what we have done in Zymomonas mobilis, which has a good correlation between the predicted RBS strengths and experimental results using dual-reporter gene FACS system, detials in our paper "
Prediction and characterization of promoters and ribosomal binding sites of Zymomonas mobilis in system biology era" : https://biotechnologyforbiofuels.biomedcentral.com/articles/10.1186/s13068-019-1399-6
Thanks. Real data are always much more convincing. It looks like RBS calculator predicts well within a medium range (eg. between 10k to 70K confidence ). Under these conditions, it will give you more confidence about the accuracy.
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