Here is the sequence logo predicted by the SAM server.
H = helix
E = sheet
C = loop (or coil)
The taller the letter at each position, the higher the probability of that specific secondary structure for that amino acid.
For example, the amino acid Valine at residue 60 is highly predicted to be part of a beta sheet. However, the Valine at residues 51 is predicted to have an equal probability of being part of a sheet or part of a loop (so it's probably not a helix).
Thanks for that, it already helped :)
btw, maybe a stupid question, but how are these secondary structures predicted?
this website has a pretty good intro:
http://www.bmm.icnet.uk/people/rob/CCP11BBS/secstrucpred.html
if you want more information about the method used to generate these sequence logos,
you can check out section 6 in http://compbio.soe.ucsc.edu/SAM_T08/faq.html
and everything you ever wanted to know about Hidden Markov Models (which is what SAM uses):
http://compbio.soe.ucsc.edu/sam.html
I hope these help!
This will take some more research tomorrow, as it doesn't read like a bedtime story...I didn't even know I wanted to know *anything* about Hidden Markov Models, LOL.
I'll have fun learning though, no doubt, your links are very much appreciated!
As soon as I get the sequence logo secondary structure predictions back from the SAM server
(http://compbio.soe.ucsc.edu/SAM_T08/faq.html)
I will post them here!