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 (The maximum input size is 200.000 characters, including the fasta headers). Click for example

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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).
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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)
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License

Web servers are available for everyone to use.

All tools are available to everyone under a CC BY-NC-ND licence. This means that users are only allowed to share (copy, distribute) for non-commercial purposes, but are not allowed to distribute adapted versions. Click to find out more about the licence.

Questions, comments, or problems?
e-RNA.org | Meyer Lab | MDC Berlin
Last update on 19. December 2022.