pocket rank differently between website and App

[suncyd]

Hello, I would like to like to ask a question that I have used PrankApp and the website to predict the same protein. But I found the final rank is different. So if there is some explanation for this result. Thank you so much.

[rdk]

@suncyd Just to confirm: I'm assuming you mean that there is a difference between the results produced by standalone P2Rank command line app and website prankweb.cz. Is that the case?

In this case I think the difference is due to the fact that the default model (i.e. trained random forest) in the standalone app is different than one that is used as default in the webappp. Webapp uses model that includes sequence conservation score among features/descriptos while standalone app uses model without conservation. If you disable "Use conservation" checkbox on the website you should get the same results as with the standalone app.

In general, model with conservation is slightly more precise.