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SPuNC

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SPuNC: Structure Prediction using Nucleotide Composition.
This site provides a method for RNA structure prediction using evolutionary patterns of nucleotide composition.

Documentation:

Examples:

Code and data:

References:

Sandra Smit, Rob Knight, and Jaap Heringa
RNA structure prediction from evolutionary patterns of nucleotide composition.
NAR (2009) 37(5):1378-86 [Online].

Maintenance:

This code is no longer actively maintained. Please, email me if you have any questions.

right_wrong

Input data

Upload a file containing an alignment or paste in an alignment
File upload:

Paste area:

Ensemble generation

fixed
    Sample size: 
redundancy
    Maximum redundancy: 
    Maximum number of structures: 
novel
    Minimum novelty: 
    Maximum number of structures: 
Remove duplicates? yesno

Method settings

Scoring function:
Weights? yesno
Reference Z-scores? trainedextreme
Top cutoff:
Base pair cutoff:

Output

Visualize? yesno

  

 

The SPuNC web server was developed by Sandra Smit, Rob Knight, and Jaap Heringa.

(c) IBIVU 2014. If you are experiencing problems with the site, please contact the webmaster.