BINDIGO Single-Pair 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