5
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I have given an input of this protein sequence:

MEPVDPRLEPWKHPGSQPKTACTTCYCKKCCFHCQVCFTTKALGISYGRKKRRQRRRPPQGSQTHQVSLSKQPTSQPRGDPTGPKE

from this website along with the option of COBEpro. Now the output sent by this site to my email is as follows:

Name: temp_prot

Amino Acids:
MEPVDPRLEPWKHPGSQPKTACTTCYCKKCCFHCQVCFTTKALGISYGRKKRRQRRRPPQGSQTHQVSLSKQPTSQPRGDPTGPKE

Predicted Continuous B-cell Epitopes:
MOST LIKELY EPITOPES:
0.82848577 39 TKALGIS CCCCCEE eee-e-e
0.82036375 39 TKALGI CCCCCE eee-e-
0.76503265 38 TTKALGI ECCCCCE eeee-e-
0.73178638 73 TSQPRGDP CCCCCCCC -eeeeeee

and a few more. Now can you tell me, if I consider the very first result, I was able to find TKALGIS in the parent sequence but could not find CCCCCEE. What is this CCCCCEE? And what does this eee-e-e mean?

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  • $\begingroup$ have you tried other software to verify? $\endgroup$ – AliceD Feb 3 '15 at 12:19
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CCCEEE etc. are the secondary structural elements. In this case, the C refers to non-strand and non-helix regions i.e loop regions rather than a coiled region. The C or E usually refers to whether the residue is coiled (C) or part of a strand (E). H would be used to denote a helix, however, in the question, it appears that there are no helices. These letters are often different in different software: it's merely a point of semantics between different software.

e or - refers to if the amino acid at that position is exposed or not (- = buried).

For the method, here is the COBEpro paper, although it does seem very technical. The help page has more easily accessible information on the output.

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  • $\begingroup$ And how is the predicted antigenic propensity score plotted? $\endgroup$ – girl101 Feb 4 '15 at 8:03
  • $\begingroup$ I'm not sure what you mean. Perhaps open a new question. $\endgroup$ – James Feb 4 '15 at 11:01

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