Displaying the information contents of structural RNA alignments: the structure logos

Jan Gorodkin, L.J. Heyer, Søren Brunak, G.D. Stormo

    Research output: Contribution to journalJournal articleResearchpeer-review

    Abstract

    We extend the standard `Sequence Logo' method of Schneider and Stevens to incorporate prior frequencies on the bases, allow for 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.dk/gorodkin/appl/slogo.html
    Original languageEnglish
    JournalCABIOS
    Volume13
    Issue number6
    Pages (from-to)583-586
    ISSN0266-7061
    Publication statusPublished - 1997

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