New analysis of sxy RNase data

I just met with the grad students to discuss their re-analysis of how RNAses sensitive to base pairing cut sxy mRNA. The new analysis is much better than what we had before. Rather than subjectively scoring sites as 'strongly cut', 'weakly cut' or 'uncut', we now have quantitative measures of the intensity of cutting at each site, and of the effect of the two mutations on this cutting.

The tricky part is how we combine the RNase data with our genetic evidence and with the secondary structure predicted by Mfold. The Mfold predictions look good, and it's easy to give more credibility to a hypothesis expressed as a drawing of a structure than to one expressed only in words or numbers (our brains love pictures). But I would feel more comfortable with the predictions if we were able to use the software at a more sophisticated level, rather than just pasting in various sequences and leaving all the settings at their defaults.