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, 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.dk/gorodkin/appl/slogo. html.

[1]  L. Gold,et al.  Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase. , 1990, Science.

[2]  G. Stormo,et al.  Identification of consensus patterns in unaligned dna and protein sequences: a large-deviation stati , 1995 .

[3]  G. Stormo,et al.  Identifying constraints on the higher-order structure of RNA: continued development and application of comparative sequence analysis methods. , 1992, Nucleic acids research.

[4]  L. Gold,et al.  Selection of high affinity RNA ligands to the bacteriophage R17 coat protein. , 1992, Journal of molecular biology.

[5]  Gary D. Stormo,et al.  Finding Common Sequence and Structure Motifs in a Set of RNA Sequences , 1997, ISMB.

[6]  Thomas M. Cover,et al.  Elements of Information Theory (Wiley Series in Telecommunications and Signal Processing) , 2006 .

[7]  L. Gold,et al.  RNA pseudoknots that inhibit human immunodeficiency virus type 1 reverse transcriptase. , 1992, Proceedings of the National Academy of Sciences of the United States of America.

[8]  Thomas M. Cover,et al.  Elements of Information Theory , 2005 .

[9]  T. D. Schneider,et al.  Sequence logos: a new way to display consensus sequences. , 1990, Nucleic acids research.

[10]  R. Nussinov,et al.  RNA pseudoknots downstream of the frameshift sites of retroviruses , 1991, Genetic Analysis: Biomolecular Engineering.

[11]  Laurie J. Heyer,et al.  Finding the most significant common sequence and structure motifs in a set of RNA sequences. , 1997, Nucleic acids research.

[12]  Gary D. Stormo,et al.  Identification of consensus patterns in unaligned DNA sequences known to be functionally related , 1990, Comput. Appl. Biosci..