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 |
- Four matches for glucocorticoid response elements are
found.
- However, the functional GRE site in the vif open reading
frame identified by Soudeyns et al. (1993) is missing.
- 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 |
- This search locates seven matches for glucocorticoid
response elements (the optimized matrix similarity thresholds
for all matrices of the GREF matrix family are lower than 0.85).
- The match list includes the functional GRE site in the
vif open reading frame (position 4995 to 5013) identified by
Soudeyns et al. (1993).
Reference:
- Soudeyns, H., Geleziunas, R., Shyamala, G., Hiscott, J., Wainberg,
M.A. (1993).
Identification of a novel glucocorticoid response element
within the genome of the human immunodeficiency virus type 1.
Virology 194, 758-768.
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