Different host organism
biseiohkawara opened this issue · comments
In original RBS calculator (web tool version, Predict Mode), we can select the other host organisms. Can we do it with ostir program?
Its possible, but your results may vary. OSTIR is calibrated on E. coli fluorescence measurements. It will spit out predictions that it thinks are E. coli RBS's. If your organism's translation initiation process is closely related to E. coli, you might get a result that works without re-calibration. You can change the anti Shine-Dalgarno sequence using the -a flag, which might help improve predictions if there's a difference.
There's a conference abstract out there that claims they used this tool to slightly improve RNA as a signal of protein abundance in a variety of prokaryotes, but I haven't actually seen the study so I can't comment much beyond that.
Let me know if you have any further questions. Otherwise, closing this issue as resolved.
Future contributions with calibration data from non E. coli model organisms welcome from any onlookers.