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 symbols. You can test the server using this sample alignment.

Or upload a file:

 Available methods 

	Evaluation against consensus structure	Pairwise evaluation
Methods based on minimum free energies
SCI and RNAeval* The SCI is defined as the consenus energy computed by RNAalifold divided by the average of the energies of the single sequences. In pairwise evaluation mode, conservation score is evaluated by comparing energies of a sequences under the constraint of being forced to fold into the structures of the other sequences to native energies.
Methods based on single structures
Base-pair distance* The base-pair distance is defined as the number of base-pairs not shared by two structures. The base-pair distance is computed as the average distance of the single sequences to a consensus sequence derived by RNAalifold.
Mountain metric Distance as the difference of two mountain functions, which give the number of base-pairs enclosing a position. Computed as the average distance of the single sequences to a consensus sequence derived by RNAalifold.
RNAdistance, full* Tree editing methods using the full represenation of RNA secondary structures (no abstraction of structural details). Computed as the average distance of the single sequences to a consensus sequence derived by RNAalifold.
RNAdistance, HIT* Tree editing methods using the HIT represenation of RNA secondary structures (no abstraction of structural details). Computed as the average distance of the single sequences to a consensus sequence derived by RNAalifold.
RNAdistance, coarse grained Tree editing methods using the coarse-grained represenation of RNA secondary structures (abstraction of structural details). Computed as the average distance of the single sequences to a consensus sequence derived by RNAalifold.
RNAdistance, wheighted coarse grained Tree editing methods using the wheighted coarse-grained represenation of RNA secondary structures (abstraction of structural details). Computed as the average distance of the single sequences to a consensus sequence derived by RNAalifold.
RNAdistance, coarse grained (Shapiro's cost) Tree editing methods using the coarse-grained represenation of RNA secondary structures (abstraction of structural details). Shapiro's cost matrix is used. Computed as the average distance of the single sequences to a consensus sequence derived by RNAalifold.
RNAdistance, wheighted coarse grained (Shapiro's cost) Tree editing methods using the wheighted coarse-grained represenation of RNA secondary structures (abstraction of structural details). Shapiro's cost matrix is used. Computed as the average distance of the single sequences to a consensus sequence derived by RNAalifold.
Methods considering the entire folding space
Ensemble distance Base-pair distance extended to compare ensembles of structures. Computed as the average distance of the single sequences to a consensus sequence derived by RNAalifold.
Mountain metric using base-pair probilities Distance as the difference of two mountain functions, which give the number of base-pairs that are expected to enclose a position on average. Computed as the average distance of the single sequences to a consensus sequence derived by RNAalifold.
RNApdist-like measure Distance measure based on the probabilities of being upstream paired, downstream paired and unpaired. Computed as the average distance of the single sequences to a consensus sequence derived by RNAalifold.

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

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

Number of random samples:  50 100 150 200

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