RBS Calculator

For an explaination of what the RBS calculator is and how it works, please see the comments in rbs_calculator.go.

To develop a model of your own, please have a look at the comments in the model.go file in the model subpackage.

Statistics compared to the orignal Salis Lab RBS Calc v2.1

The resulting values from our model differs from the original model for the following reasons:

• We may have incorrectly understood some part of the original model (our model was developed through reading research papers and converting them to code)
• Our model uses the Linearfold version of ViennaRNA (to speed up the folding process) while the orignial model doesn't. This leads to different folding structures, and hence different free-energy values.
• To find the shine-dalgarno binding site, the original model co-folds the mRNA sequence with the 16s rRNA sequence. The resulting free-energy value includes the hybridization energy of the mRNA-rRNA binding site (the shine-dalgarno site) and the free energies of the intramolecular folding of the regions upstream and downstream of the binding site on the five prime untranslated region of the mRNA. We achieve the same value by accessing the relevant hybridization free-energy value from a lookup table (which contains the hybridization free-energy values of every possilbe mRNA-rRNA combination), and adding the free-energy values that occurs from folding the upstream and downstream regions on the mRNA sequence. We're not sure if our method gives the same results as co-folding two sequences.

Statistics from the original Salis Lab RBS Calc v2.1

SUBGROUP	10-fold Error	2-fold Error	5-fold Error	AUROC	CV	KL-divergence	Max KL-divergence	N-outliers	N-states	Normalized KL-divergence	Pearson R-squared	Pearson p	RIG	RMSE	Spearman R-squared	Spearman p	intercept	slope	Sequence entropy	MC
Kosuri_PNAS_2013	0.993671	0.736777	0.924164	0.774965	1.948457	0.979609853	4.60517019	660	11	0.212719577	0.279536	0	0.351527	1.010964	0.279536	0	10.25464	-0.175	1209.7078	3742.154
Goodman_Science_2013	0.944269	0.453411	0.711638	0.53305	2.019236	0.980949194	4.60517019	185	6	0.213010411	0.006964	9.81E-14	0.093707	1.610614	0.006964	9.81E-14	10.8653	-0.037	1404.5946	526.4802
ALL	0.97032	0.602837	0.823708	0.738169	1.981913	0.900072073	4.60517019	2166	11	0.195448167	0.16712	0	0.221241	1.32865	0.16712	0	-	-	1447.568	2818.294

Statistics from our version of the Salis Lab RBS Calc v2.1

SUBGROUP	10-fold Error	2-fold Error	5-fold Error	AUROC	CV	KL-divergence	Max KL-divergence	N-outliers	N-states	Normalized KL-divergence	Pearson R-squared	Pearson p	RIG	RMSE	Spearman R-squared	Spearman p	intercept	invalid count	dataset size	slope
Kosuri_PNAS_2013	0.992202	0.47344	0.766162	0.656487	0.979322	0.997283	4.60517	71	4	0.216557	0.0924922	1.04052e-188	0.197295	1.40919	0.0924922	1.04052e-188	10.2217	0	8848	-0.115384
Goodman_Science_2013	1	1	1	0.534554	1.27911	1.78756	4.60517	57	1	0.388163	0.00535533	6.80624e-11	nan	0.482264	0.00535533	6.80624e-11	8.17327	0	7931	0.00634291
Kosuri_PNAS_2013 + Goodman_Science_2013	0.998689	0.592109	0.833065	0.855363	1.12102	1.10263	4.60517	283	4	0.239433	0.239092	0	0.267274	1.21933	0.239092	0	9.76937	0	16779	-0.0836254

Statistics have been computed using the file ./model/stats.py which has been taken from the SynBioMTS with minor modifications.