Compute Clashing Helices

Sequence Input

Enter a single nucleotide sequence (The maximum input size is 200.000 characters, including the fasta headers) Click for example [clear]

Or upload a Fasta file:

Secondary Structure Input

Enter a file containing the reference structure (in HELIX format) to which the emerging helices will be compared in order to determine the clashings

Click for example [clear]

Or upload a file in Helix format:

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 [clear]

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)

Options

Thermodynamic energy parameters

Turner, 2004 [ref]

Turner, 1999 [ref]

Andronescu, 2007 [ref]

Scaling parameters

Default

Custom:

Secondary Structure Input

Enter a file containing the reference structure (in HELIX format) to which the emerging helices will be compared in order to determine the clashings Click for example [clear]

Or upload a file in Helix format:

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.

Select the mode

Comparative

Sequence Input

Secondary Structure Input

Input Multiple Sequence Alignment

Phylogenetic Tree (Required)

Advanced Options

Non-Comparative

Sequence Input

Options

Secondary Structure Input

License