SPuNC

SPuNC: Structure Prediction using Nucleotide Composition. This site provides a method for RNA structure prediction using evolutionary patterns of nucleotide composition. Documentation: Short description of the prediction method Examples: Example alignment in fasta format (phe-tRNA) Example reference structure (phe-tRNA) Code and data: Data sets from the SPuNC paper [Browse] Cogent library is available from sourceforge SPuNC library [tar archive]. This library requires additional modules to run: RnaLib [tar archive]. 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 Maintenance: This code is no longer actively maintained.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.	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.