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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). For convenient parsing, the annotation is preceded by the amino acid symbol followed by a '|' (vertical bar).

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.

Threshold Sensitivity Specificity
-0.20 0.75 0.50
0.20 0.56 0.68
0.35 0.49 0.75
0.90 0.25 0.91
1.30 0.13 0.96

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  . .   M|.
sp_P01233_CGHB_HUMAN bepipred-1.0b epitope          2     2  -0.962  . .   E|.
sp_P01233_CGHB_HUMAN bepipred-1.0b epitope          3     3  -1.252  . .   M|.
sp_P01233_CGHB_HUMAN bepipred-1.0b epitope          4     4  -1.555  . .   F|.
sp_P01233_CGHB_HUMAN bepipred-1.0b epitope          5     5  -1.895  . .   Q|.
sp_P01233_CGHB_HUMAN bepipred-1.0b epitope          6     6  -2.226  . .   G|.
sp_P01233_CGHB_HUMAN bepipred-1.0b epitope          7     7  -2.750  . .   L|.
sp_P01233_CGHB_HUMAN bepipred-1.0b epitope          8     8  -2.961  . .   L|.
sp_P01233_CGHB_HUMAN bepipred-1.0b epitope          9     9  -3.149  . .   L|.
sp_P01233_CGHB_HUMAN bepipred-1.0b epitope         10    10  -3.149  . .   L|.
sp_P01233_CGHB_HUMAN bepipred-1.0b epitope         11    11  -3.262  . .   L|.
sp_P01233_CGHB_HUMAN bepipred-1.0b epitope         12    12  -2.765  . .   L|.
sp_P01233_CGHB_HUMAN bepipred-1.0b epitope         13    13  -2.204  . .   L|.
sp_P01233_CGHB_HUMAN bepipred-1.0b epitope         14    14  -1.482  . .   S|.
sp_P01233_CGHB_HUMAN bepipred-1.0b epitope         15    15  -1.086  . .   M|.
sp_P01233_CGHB_HUMAN bepipred-1.0b epitope         16    16  -0.518  . .   G|.
sp_P01233_CGHB_HUMAN bepipred-1.0b epitope         17    17   0.094  . .   G|.
sp_P01233_CGHB_HUMAN bepipred-1.0b epitope         18    18   0.780  . .   T|E
sp_P01233_CGHB_HUMAN bepipred-1.0b epitope         19    19   1.013  . .   W|E
sp_P01233_CGHB_HUMAN bepipred-1.0b epitope         20    20   1.221  . .   A|E
sp_P01233_CGHB_HUMAN bepipred-1.0b epitope         21    21   1.006  . .   S|E
sp_P01233_CGHB_HUMAN bepipred-1.0b epitope         22    22   1.047  . .   K|E
sp_P01233_CGHB_HUMAN bepipred-1.0b epitope         23    23   0.817  . .   E|E
sp_P01233_CGHB_HUMAN bepipred-1.0b epitope         24    24   1.004  . .   P|E
sp_P01233_CGHB_HUMAN bepipred-1.0b epitope         25    25   1.078  . .   L|E
sp_P01233_CGHB_HUMAN bepipred-1.0b epitope         26    26   0.925  . .   R|E
sp_P01233_CGHB_HUMAN bepipred-1.0b epitope         27    27   0.674  . .   P|E
...




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