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© Oxford University Press

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

J. Gorodkin , L.J. Heyer 1, S. Brunak and G.D. Storomo 2

Center for Biological Sequence Analysis, The Technical University of Denmark Building 206, 2800 Lyngby, DK-2800, Denmark
1Department of Applied Mathematics University of Colorado Boulder, CO 80309, USA
2Department of Molecular, Cellular and Developmental Biology, University of Colorado Boulder, CO 80309, USA

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 ft,r 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. 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.

AVAILABILITY:: 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.

CONTACT:: E-mail: gorodkin{at}cbs.dtu.dk

Received on March 5, 1997; revised on May 10, 1997; accepted on May 14, 1997

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