ShapeSorter the first computational method for detecting functional RNA structure features that are supported both by evolutionary evidence and experimental SHAPE-probing evidence. ShapeSorter is capable of capturing RNA structure features due to RNA structure heterogeneity, transient RNA structure features as well as features of pseudo-knotted RNA structures. ShapeSorter employs a purely probabilistic framework that seamlessly integrates both evolutionary as well experimental SHAPE-probing evidence. It returns as output helices (i.e. stretches of consecutive base-pairs) that can be readily ranked by their estimated p-values.

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:

Input SHAPE probing data

Paste a SHAPE file 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

Not changing any of the following entries will result in the default version of ShapeSorter being used.

Use all sequences Use not only reference sequence for proposing conserved helices
Normalization Normalize helices by their length
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: