Displaying the in formation contents of structural RNA alignments: the structure logos

Abstract

We extend the standard ‘Sequence Logo’method of Schneider and Stevens (Nucleic Acids Res., 18, 6097–6100, 1990) to incorporate prior frequencies on the bases, allow ft,r gaps in the alignments, and indicate the mutual information of base-paired regions in RNA. Given an alignment of RNA sequences with the base pairings indicated, the program will calculate the information at each position. including the mutual information of the base pairs. and display the results in a ‘Structure Logo’. Alignments without base pairing can also be displayed in a ‘Sequence Logo’. but still allowing gaps and incorporating prior frequencies if desired. The code is available from, and an Internet server can be used to run the program at, http://www.cbs.dtu.dklgorodkin/appl/slogo.html. E-mail: gorodkin@cbs.dtu.dk