whitehead/plaac

Prion-Like Amino Acid Composition

plaac's Issues

Which column should I use to determine whether a protein is prion-like or not?

Hi, Thanks for providing this user-friendly software for prion-like sequence detection. My question is how to judge a protein as a whole is prion-like or not? To do this, which column from the result file should I use and what cut-off should I set? Waiting for your reply and thanks!

How the transition probabilities (0.02 and 0.001) were determined?

Thanks very much for the amazing software. According to the article (Cell, 2009), 'The transition probability from PrD to background was set to 0.02 and the transition probability from background to PrD state was set to 0.001. Initial probabilities for PrD and background were set to 0.05 and 0.95, respectively.'

A domain is PrD is considered as a small probability event, I think it is the reason why initial probabilities were set to 0.05 and 0.95, respectively. But I am a little confused about how the transition probabilities were decided?

http://plaac.wi.mit.edu/ is down - can you fix?

please?

thanks

Production not processing TAIR file correctly

Download:

ftp://ftp.arabidopsis.org/home/tair/Proteins/TAIR10_protein_lists/TAIR10_pep_20101214

upload and try and run with default parameters, get Internal Server Error

Maybe a server-side problem?