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Optimized thresholds versus fixed thresholds

Searching glucocorticoid response elements (GRE) in a HIV-1 sequence (HIVBRUCG) yields the following results:

- With a fixed matrix similarity threshold of 0.85

Inspecting sequence HIVBRUCG [K02013] (1 - 9229):

   Family/matrix Opt. Position Str. Core sim. Matrix sim. Sequence
from - to anchor
  V$GREF/PRE.01 0.84 740 - 758 749 (-) 1.000 0.887 ttgcccctggaTGTTctgc
  V$GREF/PRE.01 0.84 6865 - 6883 6874 (-) 1.000 0.882 tatttccaaatTGTTctct
  V$GREF/PRE.01 0.84 7470 - 7488 7479 (-) 1.000 0.869 cctcagcaaatTGTTctgc
  V$GREF/PRE.01 0.84 8866 - 8884 8875 (-) 1.000 0.888 taacaagctggTGTTctct


- With optimized matrix similarity threshold

Inspecting sequence HIVBRUCG [K02013] (1 - 9229):

   Family/matrix Opt. Position Str. Core sim. Matrix sim. Sequence
from - to anchor
  V$GREF/PRE.01 0.84 740 - 758 749 (-) 1.000 0.887 ttgcccctggaTGTTctgc
  V$GREF/PRE.01 0.84 3195 - 3213 3204 (-) 0.750 0.842 tgggcacccctCGTTcttg
  V$GREF/GRE.01 0.81 4995 - 5013 5004 (-) 0.927 0.825 ggctaactatatGTCCtaa
  V$GREF/PRE.01 0.84 6865 - 6883 6874 (-) 1.000 0.882 tatttccaaatTGTTctct
  V$GREF/ARE.01 0.80 7197 - 7215 7206 (-) 1.000 0.819 ctcggacccatTGTTgtta
  V$GREF/PRE.01 0.84 7470 - 7488 7479 (-) 1.000 0.869 cctcagcaaatTGTTctgc
  V$GREF/PRE.01 0.84 8866 - 8884 8875 (-) 1.000 0.888 taacaagctggTGTTctct

Reference: