CoBold ['ko:bɔlt]
Predict RNA secondary structure features that could either aid or prevent the co-transcriptional formation of a known reference RNA secondary structure
MANUSCRIPT: Alignment files for our published analysis: Here. The source code of CoBold will be available upon publicatin of manuscript.
EXAMPLES LOADED: Click Submit to see webserver in action, or Reset to submit own input.

Main CoBold

Comparative

Sequence Input

Enter a single nucleotide sequence (with optional fasta header, up to 50kb):

MISSING INPUT: Please paste or upload input data.

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

MISSING INPUT: Please paste or upload structure data.

Or upload a file in Helix format:

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 or upload input MSA data.
OR Upload a file:

Phylogenetic Tree (Required)

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 or upload tree 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:

Non-Comparative

Sequence Input

Enter a single nucleotide sequence (with optional fasta header, up to 50kb):

MISSING INPUT: Please paste or upload input data.

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

MISSING INPUT: Please paste or upload structure data.

Or upload a file in Helix format:

Options

Thermodynamic energy parameters

Turner, 2004 [ref]

Turner, 1999 [ref]

Andronescu, 2007 [ref]

Scaling parameters

Default

Custom:

New field set
Other parameters

Minimum helix length

Minimum clash overlap

  • Please be patient when submitting long sequences. A 1500 nt sequence will take roughly 20 seconds, and a 3000 nt sequence may take up to 3 minutes.
(Optional) Your e-mail for job completion notice: