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Output format
DESCRIPTION
The output conforms to the GFF format. For each input sequence the server outputs a prediction score and annotation for every residue. The positions of the linear B-cell epitopes are predicted to be located at the residues with the highest scores. The annotation, given in the column denoted "?", is determined by the given threshold for the scores. A residue annotated with an "E" is predicted as being part of a linear B-cell epitope (score above threshold), where an "." represents a residue predicted not to be part of an epitope (score below threshold).
The table below shows the relationship between selected thresholds and the sensitivity/specificity of the prediction method, calculated on basis of the epitope/non-epitope predictions. The table is based on a large benchmark calculation containing close to 85 B cell epitopes.
The table above can be used to set a suitable threshold; reflecting the needs of the user (see Instructions).
EXAMPLE OUTPUT##gff-version 2 ##source-version bepipred-1.0b ##date 2006-10-23 ##Type Protein sp_P01233_CGHB_HUMAN ##Protein sp_P01233_CGHB_HUMAN ##MEMFQGLLLLLLLSMGGTWASKEPLRPRCRPINATLAVEKEGCPVCITVNTTICAGYCPT ##MTRVLQGVLPALPQVVCNYRDVRFESIRLPGCPRGVNPVVSYAVALSCQCALCRRSTTDC ##GGPKDHPLTCDDPRFQDSSSSKAPPPSLPSPSRLPGPSDTPILPQ ##end-Protein # seqname source feature start end score N/A ? # --------------------------------------------------------------------------- sp_P01233_CGHB_HUMAN bepipred-1.0b epitope 1 1 -1.140 . . . sp_P01233_CGHB_HUMAN bepipred-1.0b epitope 2 2 -0.962 . . . sp_P01233_CGHB_HUMAN bepipred-1.0b epitope 3 3 -1.252 . . . sp_P01233_CGHB_HUMAN bepipred-1.0b epitope 4 4 -1.555 . . . sp_P01233_CGHB_HUMAN bepipred-1.0b epitope 5 5 -1.895 . . . sp_P01233_CGHB_HUMAN bepipred-1.0b epitope 6 6 -2.226 . . . sp_P01233_CGHB_HUMAN bepipred-1.0b epitope 7 7 -2.750 . . . sp_P01233_CGHB_HUMAN bepipred-1.0b epitope 8 8 -2.961 . . . sp_P01233_CGHB_HUMAN bepipred-1.0b epitope 9 9 -3.149 . . . sp_P01233_CGHB_HUMAN bepipred-1.0b epitope 10 10 -3.149 . . . sp_P01233_CGHB_HUMAN bepipred-1.0b epitope 11 11 -3.262 . . . sp_P01233_CGHB_HUMAN bepipred-1.0b epitope 12 12 -2.765 . . . sp_P01233_CGHB_HUMAN bepipred-1.0b epitope 13 13 -2.204 . . . sp_P01233_CGHB_HUMAN bepipred-1.0b epitope 14 14 -1.482 . . . sp_P01233_CGHB_HUMAN bepipred-1.0b epitope 15 15 -1.086 . . . sp_P01233_CGHB_HUMAN bepipred-1.0b epitope 16 16 -0.518 . . . sp_P01233_CGHB_HUMAN bepipred-1.0b epitope 17 17 0.094 . . . sp_P01233_CGHB_HUMAN bepipred-1.0b epitope 18 18 0.780 . . E sp_P01233_CGHB_HUMAN bepipred-1.0b epitope 19 19 1.013 . . E sp_P01233_CGHB_HUMAN bepipred-1.0b epitope 20 20 1.221 . . E sp_P01233_CGHB_HUMAN bepipred-1.0b epitope 21 21 1.006 . . E sp_P01233_CGHB_HUMAN bepipred-1.0b epitope 22 22 1.047 . . E sp_P01233_CGHB_HUMAN bepipred-1.0b epitope 23 23 0.817 . . E sp_P01233_CGHB_HUMAN bepipred-1.0b epitope 24 24 1.004 . . E sp_P01233_CGHB_HUMAN bepipred-1.0b epitope 25 25 1.078 . . E sp_P01233_CGHB_HUMAN bepipred-1.0b epitope 26 26 0.925 . . E sp_P01233_CGHB_HUMAN bepipred-1.0b epitope 27 27 0.674 . . E ... GETTING HELP
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