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.

**Batch** takes a file containing multiple *s* and *t* pairs and outputs the
optimal Delta G (kcal/mol) for each pair.
There are restrictions: all of the *s*'s must be the same length, and all of the *t*'s
must be the same length, but the *s*'s need not be the same length as the *t*'s.

gggggggggggg
ccccccccc gugugugugugu gugugugug acgacgacgacg cgucgucgu |

Then length of s=12 and length of t=9. The output will contain the delta G's in the format:

s: gggggggggggg, t: ccccccccc, Delta G: -23.6
s: gugugugugugu, t: gugugugug, Delta G: -0.2 s: acgacgacgacg, t: cgucgucgu, Delta G: -15.1 |