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Biophysical modeling leads to newly discovered molecular interactions between the ribosome and mRNA at standby sites, and predicts how sequences upstream of the Shine-Dalgarno control translation rate and post-transcriptional regulation.

Espah Borujeni, A., Channarasappa A.S., and Salis H.M., (2013) Translation Rate is Controlled by Coupled Trade-offs between Site Accessibility, Selective RNA unfolding and Sliding at Upstream Standby Sites, Nucleic Acid Research, v41 (21)

Learn the origins of "context effects" between promoters and RBSs, and how structured mRNAs can coax the ribosome into performing regulatory tricks.

The Small RNA Calculator

Click here to try an example!


Small RNA Sequence [?]
Small RNA Sequence: enter the nucleotide sequence of a small RNA that binds to mRNA and regulates translation initiation, using A/G/C/T/U. (required).

mRNA Sequence [?]
mRNA Sequence: enter the nucleotide sequence of an mRNA transcript, using A/G/C/T/U. (required)

Organism or (16S rRNA) [?]
Organism or 16S rRNA sequence: choose a bacterial species by typing in the first 3 letters of its name and selecting it from the list. Alternatively, you may enter the last 9 nucleotides of the 16S rRNA, using A/G/C/T/U. (required)
(start typing)

For Non-Commercial Use Only
Design Jobs: 1 queued, 40 currently running
Developed by Amin Espah Borujeni and Howard Salis.
Please inquire about proper citation before using these results in a publication.
Have a Question? Our Documentation, Publications, and References may have your answer!
We gratefully acknowledge research funding from the Defense Advanced Research Projects Agency, the National Science Foundation, the Office of Naval Research, and an Amazon AWS Research Grant.
Computational resources are provided by the AWS Elastic Compute Cloud.
Method online since January 10th, 2011.