realbigws / predict_property Goto Github PK

Hi,
First of all, thank you for this user-friendly tool that you provided. I like it a lot.
Then, could you please give some more help on the tm8 files ?
You say :
"#TopoPred_TM8: 8-state transmembrane topology prediction results by no_profile mode
#probabilities are in the order of H E C I L F X _, the 8 transmembrane topology types used
in PDBTM "
But I don't see how the letters correspond to what I find in the PDBTM database
which is :
Legend: Inside - Membrane - Outside -Re-entrant loop - Beta barrel - inside - Periplasm - Interfacial helix
ex : https://pdbtm.unitmp.org/entry/6edq

What are each column ?

Thanks

I tried to predict disordered regions in the following input protein sequence (saved in my_seq.fasta):

>my_seq
DIQMTQSPSSLSASVGDRVTITCRASQDVNTAVAWYQQKPGKAPKLLIYSASFLYSGVPSRFSGSRSGTDFTLTISSLQPEDFATYYCQQHYTTPPTFGQGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

The command I used was: ./Predict_Property.sh -i my_seq.fasta

In one of the output files (my_seq.diso), we can see that the positions 156~160 have high probabilities to be disordered.

 156 S * 0.993 
 157 G * 0.998 
 158 N * 0.999 
 159 S * 0.999 
 160 Q * 0.999 

However, if I use the RaptorX web server to do the prediction using the same input sequence, the predicted disorder probability is much lower:

 156 S . 0.456 
 157 G * 0.511 
 158 N . 0.500 
 159 S . 0.421 
 160 Q . 0.307 

Based on what we know about my_seq, the prediction from the RaptorX web server is more likely to be correct. Could you check why the predictions are different?

Thank you very much!