Visualizing bacterial tRNA identity determinants and antideterminants using function logos and inverse function logos

Freyhult, E., Moulton, V. and Ardell, D. (2006) Visualizing bacterial tRNA identity determinants and antideterminants using function logos and inverse function logos. Nucleic Acids Research, 34 (3). pp. 905-916. ISSN 0305-1048

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Abstract

Sequence logos are stacked bar graphs that generalize the notion of consensus sequence. They employ entropy statistics very effectively to display variation in a structural alignment of sequences of a common function, while emphasizing its over-represented features. Yet sequence logos cannot display features that distinguish functional subclasses within a structurally related superfamily nor do they display under-represented features. We introduce two extensions to address these needs: function logos and inverse logos. Function logos display subfunctions that are over-represented among sequences carrying a specific feature. Inverse logos generalize both sequence logos and function logos by displaying under-represented, rather than over-represented, features or functions in structural alignments. To make inverse logos, a compositional inverse is applied to the feature or function frequency distributions before logo construction, where a compositional inverse is a mathematical transform that makes common features or functions rare and vice versa. We applied these methods to a database of structurally aligned bacterial tDNAs to create highly condensed, birds-eye views of potentially all so-called identity determinants and antideterminants that confer specific amino acid charging or initiator function on tRNAs in bacteria. We recovered both known and a few potentially novel identity elements. Function logos and inverse logos are useful tools for exploratory bioinformatic analysis of structure–function relationships in sequence families and superfamilies.

Item Type: Article
Faculty \ School: Faculty of Science > School of Computing Sciences
University of East Anglia > Faculty of Science > Research Groups > Computational Biology (subgroups are shown below) > Computational biology of RNA
University of East Anglia > Faculty of Science > Research Groups > Computational Biology (subgroups are shown below) > Phylogenetics
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Depositing User: Vishal Gautam
Date Deposited: 21 May 2011 12:59
Last Modified: 05 Sep 2018 16:31
URI: https://ueaeprints.uea.ac.uk/id/eprint/23641
DOI: 10.1093/nar/gkj478

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