RILogo web server : Submit

RILogo - web server

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.

Submit

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 treeMI^W+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.
% Start/end colors (RGB hex format) of the color gradient for the mutual information of % base-paired columns. While the start and end colors ar given as RGB values, % the actual gradient is calculated in HSV color space. arcs_color_from = #00ff00 arcs_color_to = #ff0000 % Color of arcs, if no MI is used, i.e. for only one sequence in the input arcs_color_nomi = #0261c8 % Colors (RGB hex format) for nucleotide characters in logos or single sequences color_A = #14e01a color_C = #007fff color_G = #ff6321 color_U = #b7140b % The color of the letter M, used to donate the mutual information (MI) in sequence logos color_M = #07570b % If true, then no M characters for the MI will be printed in the sequence logos no_M = false % Switches numbering of nucleotides draw_rulers = true % Enable no_chars to print small circles instead of nucleotide letters or sequence logos no_chars = false % Enable logarithmic color gradient for the coloring of arcs and lines by the MI log_colors = true % Enable drawing of the color gradient legend for MI values draw_legend_mi = true

Submit

Multiple Sequence Alignment*

2nd Multiple Sequence Alignment

Mutual Information measure:

Optional parameters

Phylogenetic tree

Weighting of bp frequencies by tree distances:

Customization of output