RNA Home Aalberts' Lab BINDIGO
  Single Pair Batch Mode

Welcome to the BINDIGO Server

In order to accommodate a variety of users, we have provided two separate versions of our BINDIGO tool.

Select a BINDIGO version:

Two Sequences Input s and t. BINDIGO reports the optimal alignment and free energy. This tool is ideal for getting familiar with BINDIGO and performing single experiments.
Multiple Pairings Input a file of multiple s and t pairs. BINDIGO reports the optimal free energy for each. This tool is ideal for performing multiple computations in succession.


Many cellular processes rely on an RNA fragment binding to an RNA target; examples include small nuclear RNAs binding to splice junctions (the example in our paper), microRNAs, retrotransposons, and short interfering RNAs. (DNA microarrays also work on the same physical principle.)

To find the optimal RNA-RNA bound state of strings of lengths N1 and N2, a number of authors have modified RNA folding algorithms to compute the free energy. All of them take time O((N1+N2)³). Our BINDIGO does the same in time O(N1×N2) because it is designed for binding, not folding.

BINDIGO implements the Turner free energy rules for RNA-RNA binding in a dynamic programming algorithm. We have also introduced a new heuristic for calculating the large asymmetric loops.

Read our paper and supplementary material

Efficient Computation of Optimal Oligo-RNA Binding, Nathan O. Hodas '04 and Daniel P. Aalberts, Nucleic Acids Research 32, 6636-6642 (2004).