Transat detects conserved helices of high statistical significance, including pseudo-knotted, transient and alternative structures. Given a multiple sequence alignment, Transat will recover all possible helices and determine the statistical probability of the helix existing based on its phylogeny-based evolutionary likelihood.

Input Multiple Sequence Alignment

Paste a multiple sequence alignment of one or more sequences in FASTA format (up to 200kb total). Click for example

MISSING INPUT: Please paste of upload input data.
OR Upload a file:
(Optional) Your e-mail for job completion notice:

Phylogenetic Tree (Optional)

Paste a phylogeny tree in Newick format. All species must match those in both alignments. Click for example

One will be computed if no tree is given (and can be retrieved in the results tar-ball).
MISSING INPUT: Please paste of upload input data.
OR Upload a file:

Advanced Options

Minimum stem length (Only helices with this number of basepairs will be output)
Minimum loop length (Only helices with basepairs at least this many basepairs apart will be output)
Maximum P-value threshold (Does not output helices with P-values above this threshold.)
Minimum log likelihood threshold (Does not output helices with log likelihoods below this threshold.)
Approximate minimum P-value (Controls the number of randomlized trials. The smaller the value, the longer the job takes.)
No P-values (Completely skips P-value computation if checked, much faster)
Output dot-bracket (Outputs full dot-bracket format in output if checked, significantly increases file size)
(Optional) Your e-mail for job completion notice: