Work

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

Year: 1997

Type: article

Abstract: 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.

Source: Computer applications in the biosciences

DOI: 10.1093/bioinformatics/13.6.583

Authors: J. Gorodkin, L.J. Heyer, S. Brunak, G.D. Storomo

Institutions: Technical University of Denmark, University of Colorado Boulder, University of Colorado System

Language: English

Topic: RNA and protein synthesis mechanisms

Subfield: Molecular Biology

Field: Biochemistry, Genetics and Molecular Biology

Domain: Life Sciences

Open Access status: bronze

Funders: National Research Foundation, Danmarks Grundforskningsfond, National Institutes of Health, National Human Genome Research Institute

Award: DNA PATTERN IDENTIFICATION AND ANALYSIS