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A customized ViennaRNA forna web-server to display RNA triplexes as represented in the TriplexRNA database.

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forna-serve

Forna-serve wraps a custom ViennaRNA forna web-server, to display and edit RNA triplexes as shown in the TriplexRNA database.

Installation requirements

The only requirement is Docker, which can be installed in different ways depending on the underlying operative system:

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Run forna-serve

To run forna-serve, you need to run its docker container. Type:

docker run -d -p 9090:8080 quay.io/bagnacan/forna-serve

The forna-serve web-service is now listening on your host's port 9090. You can test its docker container by opening your browser, and type:

localhost:9090/ping

You should receive a pong reply. If so, the service is up and running!
You can now send proper forna queries to visualize and edit RNA triplexes.

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Usage

Here we explain the URL syntax that is required for requesting RNA triplex visualizations, and provide a sample query.

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URL syntax

The syntax to visualize RNA molecules is based on the one defined by forna, and extended to distinguish the different RNAs of a triplex:

  1. Host
    If you are running the forna-serve container on your localhost, this will likely look like http://localhost:9090/

  2. Triplex identifier
    A name for the visualized triplex T, which must be provided as ?id=url/T

  3. Sequence
    The full sequence S of the complex, to be provided as &sequence=S

  4. Structure
    The dot-bracket notation D of the complex, to be provided by &structure=D

  5. Target gene
    The target gene name G, &gene=G

  6. 1st miRNA
    The 1st miRNA name M1, &mirna1=M1

  7. 2nd miRNA
    The 2nd miRNA name M2, &mirna2=M2

  8. Colors
    The color scheme of the 3 different segments, to be counted in nucleotides.
    Supposing that:

  • G should be colored lightgrey, its sequence starts at nt. 1, and ends at nt. GL
  • M1 should be colored lightgreen, its sequence starts at nt. GL+1 and ends at nt. M1L
  • M2 should be colored red, its sequence starts at nt. M1L+1 and ends at nt. M2L
    The scheme of the triplex T will be: &colors=>T\n1-GL:lightgrey\nGL+1-M1L:lightgreen\nM1L+1-M2L:red

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Example

Using the aforementioned syntax, we compose a URL to display the RNA triplex 97544.

The triplex is formed by Human (hg19) target gene E2F1, miRNA hsa-miR-205, and miRNA hsa-miR-342-3p.

  1. Host
    http://localhost:9090
  2. Triplex identifier
    ?id=url/97544
  3. Sequence
    &sequence=ccgggggugaaugugugugagcaugugugugugcauguaccggggaaugaagguuccuucauuccaccggagucugucucacacagaaaucgcacccgu
    Where:
    • E2F1 ccgggggugaaugugugugagcaugugugugugcauguaccggggaaugaaggu
    • hsa-miR-205 uccuucauuccaccggagucug
    • hsa-miR-342-3p ucucacacagaaaucgcacccgu
  4. Structure
    &structure=.((((.((((.(.(((((((((((((......)))))..((((((((((((((..)))))))))).)))).......))))))))..).)))).)))).
  5. Target gene
    &gene=E2F1
  6. 1st miRNA
    &mirna1=hsa-miR-205
  7. 2nd miRNA
    &mirna2=hsa-miR-342-3p
  8. Colors
    &colors=%3E97544\n1-54:lightgray\n55-76:lightgreen\n77-99:red
    Where:
    • E2F1's sequence starts at nt. 1 and ends at nt. 54 (lightgray)
    • hsa-miR-205's sequence starts at nt. 5 and ends at nt. 76 (lightgreen)
    • hsa-miR-342-3p's sequence starts at nt. 77 and ends at nt. 99 (red)

You can now assemble the full URL, and type it in the browser:

http://localhost:9090/?id=url/97544&sequence=ccgggggugaaugugugugagcaugugugugugcauguaccggggaaugaagguuccuucauuccaccggagucugucucacacagaaaucgcacccgu&structure=.((((.((((.(.(((((((((((((......)))))..((((((((((((((..)))))))))).)))).......))))))))..).)))).)))).&gene=E2F1&mirna1=hsa-miR-205&mirna2=hsa-miR-342-3p&colors=%3E97544\n1-54:lightgray\n55-76:lightgreen\n77-99:red

You will visualize something like this:

Sample triplex E2F1 + hsa-miR-205 + hsa-miR-342-3p

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A customized ViennaRNA forna web-server to display RNA triplexes as represented in the TriplexRNA database.

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