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  Single Pair Batch Mode

BINDIGO 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.


Input file:
Length of s:
Length of t:
Number of pairs:

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.

For example, given the input file, input.test:


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