RNA Home | Aalberts' Lab | BINDIGO | |||
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Single Pair | Batch Mode |

NOTE: BINDIGO has an inherent directionality. It starts binding at the 5' end of string s and continues towards its 3' end (thus binding 3' to 5' of string t). To reverse this directionality, simply swap the s and t sequences. In the rare cases where the optimal folds may disagree, the best of the two is the correct fold.

The versions of BINDIGO found on this page all take two input
sequences, s and t, and fold them together. Strings *s* and
*t* are not case sensitive, but must be composed of characters A,
C, G, T, or U. Both strings are input in standard 5' to 3' order. See
below for complete descriptions of the different options.

**Output optimal dG** reports the optimal free energy and the
secondary structure. For example if *s*=cgagacucagu and
*t*=gcaguacguacgu:

`
Delta G: -1.1 kcal/mol
s: cgACacu*cAGU
t: UGCAUgcC*ugaCg
`
Notice the notation that paired bases are in lowercase, unpaired bases
are in uppercase, and asymmetric loops are balanced by *'s.

**Old Terminal Mismatch Rule Optimal dG ** is the same as the
first EXCEPT it uses the older terminal mismatch rules used by
Pairfold and other older folding algorithms.

**Output F(i,j)** outputs the F matrix, allowing the scrutiny
of the DeltaG's resulting from different possible alignments. F(i,j)
is the free energy of the best way to align *s* and *t* such
that *s*[i] and *t*[j] are the last paired bases. The ith
row and jth column of the matrix displayed corresponds to F(i,j), with
F(0,0) and the top row and leftmost column representing no binding.
While all units are in kcal/mol, the number 298.21 is a sufficiently
large number to represent no binding.

If *s*=gggg and *t*=cccc

`
298.21 298.21 298.21 298.21 298.21
298.21 2.5 1.7 1.7 2
298.21 2.5 -0.8 -1.6 -1.3
298.21 2.5 -0.8 -4.1 -4.6
298.21 3.8 0.5 -2.8 -5.8
`