DISPLAYING THE INFORMATION CONTENTS OF STRUCTURAL RNA ALIGNMENTS - THE STRUCTURE LOGOS

Motivation: 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 for gaps in the alignments, and indicate the mutual information of base-paired regions in RNA, Results : Given an alignment of RNA sequences with the base pairings indicated , the program will calculate the information at each position, includi ng the mutual information of the base pairs, and display the results i n a 'Structure Logo'. Alignments without base pairing can also be disp layed in a 'Sequence Logo', but still allowing gaps and incorporating prior frequencies if desired. Availability: The code is available from , and an Internet server can be used to run the program at, http://www .cbs.dtu.dk/gorodkin/appl/slogo.html. Contact: E-mail: gorodkin@cbs.dt u.dk.