RILogo creates RNA-RNA interaction logos for two RNAs. The input are either two single sequences or two multiple sequence alignments with annoation of intra- or intermolecular base pairing between the two RNAs. RILogo displays sequence conservation by a sequence logo for each RNA and structure conservation by the mutual information of the secondary structure base pairings. RILogo supports four different methods for calculating the mutual information.
See the Help page for input formats and examples. RILogo is free of charge and also available for download as an open source standalone program.


Please fill out the submission form and click the Submit button. Input fields marked with a * are required. (Load Example Data)

Multiple Sequence Alignment*

Enter your multiple sequence alignment with structure annotation here. Either use the text area or upload a file.
Supported formats are Stockholm, Clustal or Fasta.
In Clustal and Fasta format, the secondary structure annotation must have the sequence name structure.
The alignment can also contain both interacting RNAs.
In that case, both sequences belonging to one species must be separated by the '&' character. [?]
Upload alignment file:

2nd Multiple Sequence Alignment

If the first alignment contains only one RNA, then insert the second alignment here. Either use the text area or upload a file. [?]
Upload alignment file:

Mutual Information measure:

RILogo implements four different measures for the mutual information of base pairs.
Please refer to the paper for the exact definitions. [?]

Optional parameters

Phylogenetic tree

Specify a custom phylogenetic tree for the sequences in the alignment.
The tree must be in Newick format. Either use the text area or upload a file. [?]
Upload tree file:

Weighting of bp frequencies by tree distances:

Only for treeMI and treeMIW+P. Switches weighting by tree distances, rather than number of sequences.
This means, that fully conserved base pairs will get an MI of zero. [?]

Customization of output

This configuration file can be used to change the default graphical parameters for the output.