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GRAPHICAL OUTPUT-3
(Threshold Vs Best Scoring Subsequence
Distribution Profile)
An example out put of Antigen 85B (M. tuberculosis).
The figure appears
only during sub sequence analysis. Here the highest scoring peptide
frame is treated as representative of whole query sub sequence. Top
red line is the entire threshold
range and the blue line against each allele represents threshold value
at or above which the query sub sequence will be predicted
as binder.
The figure is useful
for experienced users in selecting threshold, while locating promiscuous
binding regions.
e.g.
Sequence :
FFVASDREPLMN
Sub sequences:
FFVASDREP
Score: 1.2
FVASDREPL
Score: 1.0
VASDREPLM
Score: 1.4
ASDREPLMN
Score: 0.8
The highest scorer
i.e. " VASDREPLM "
will be plotted as representative of sequence. The blue line represents
the threshold at or below which this subsequent will be predicted as binder.
But to me the other
two figures are more informative because
i) They are not
restricted to highest scoring peptide frame hence will deliver true picture
of subsequent.
ii) The location
and score of highest scoring subsequent can be determined.
iii) Other binding
frames close to threshold or generated by one or two amino acid shift in
highest scoring sequence can also be easily located.
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