Welcome to the Structure Conservation Analysis web server. It will help you to detect evolutionarily conserved RNA secondary structures in multiple sequence alignments. Current limits are 2000 nt and 50 sequences for an alignment.

Simply paste or upload your alignment(s) below and click Proceed. Accepted alignment formats are CLUSTAL W and FASTA (will be detected automatically). To get more information on the meaning of the options click the help symbols. You can test the server using this sample alignment.


 Available methods 
Evaluation against
consensus structure
Pairwise evaluation
Methods based on minimum free energies
SCI and RNAeval* help
Methods based on single structures
Base-pair distance* help
Mountain metric help
RNAdistance, full* help
RNAdistance, HIT* help
RNAdistance, coarse grained help
RNAdistance, wheighted coarse grained help
RNAdistance, coarse grained (Shapiro's cost) help
RNAdistance, wheighted coarse grained (Shapiro's cost) help
Methods considering the entire folding space
Ensemble distance help
Mountain metric using base-pair probilities help
RNApdist-like measure help

* Recommended methods, that showed good performance in our benchmark.

 Use sequences without gaps for tree editing methods (pairwise comparisons only).

Number of random samples: 

Notification via e-mail upon complete of the job (optional):