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Table 3 RNA FRABASE 2.0, 1.0 and FASTR3D - performance comparison.

From: RNA FRABASE 2.0: an advanced web-accessible database with the capacity to search the three-dimensional fragments within RNA structures

Pattern (query) Description of the query pattern and advanced options (in RNA FRABASE 2.0) Number of results
   RNA FRABASE 2.0 RNA FRABASE 1.0 FASTR3D
>strand1
GAcUgAAgAuc
tRNA anticodon loop (only sequence) default options 61 60 55
>strand1
GacUgAAgAuc
(.........)
tRNA anticodon loop
a) default options
b) add through-space interactions: ON
34
47
34
-
32
-
>strand1
NNNGNRANNN
(((....)))
Hairpin GNRA loop
a) default options
b) include all models: ON
2120
2125
1680
-
1498
-
>strand1
NNNGNRANNN
((?....?))
Hairpin GNRA loop default options 2392 - -
>strand1
^(((((((((($
>strand2
^))))))))))$
Decamer duplex default options 67 - -
>strand1
^(((((((
>strand2
)))))))....$
tRNA acceptor stem default options 143 - -
>strand1
NNNANNN
(((.(((
>strand2
NNNNNN
))))))
Duplex with a single adenosine bulge:
a) default options b)
strand shift operation: ON
356
606
287
-
-
-
>strand1
(......(
>strand2
).....)
Internal loop (E loop in 5S rRNA)
a) default options
b) strand shift operation: ON
258
528
226
-
209
-
>strand1
((.......((
>strand2
))....((
>strand3
))..))
Three-way junction loop (in ribozyme) default options 12 11 14
>strand1
(((....).((
>strand2
))...((
>strand3
)).))
Three-way junction loop (in hammerhead)
a) default options
b) strand shift operation: ON
2
4
2
-
2
-
>strand1
(((.[[[[[[)))
>strand2
(((.]]]]]])))
Kissing loop default options 57 52 48