pLogo: a probabilistic approach to visualizing sequence motifs

Journal name:
Nature Methods
Volume:
10,
Pages:
1211–1212
Year published:
DOI:
doi:10.1038/nmeth.2646
Received
Accepted
Published online

Methods for visualizing protein or nucleic acid motifs have traditionally relied upon residue frequencies to graphically scale character heights. We describe the pLogo, a motif visualization in which residue heights are scaled relative to their statistical significance. A pLogo generation tool is publicly available at http://plogo.uconn.edu/ and supports real-time conditional probability calculations and visualizations.

At a glance

Figures

  1. Comparison of sequence logo visualizations for the pLogo, iceLogo and WebLogo tools.
    Figure 1: Comparison of sequence logo visualizations for the pLogo, iceLogo and WebLogo tools.

    312 human Src tyrosine phosphorylation sites (left) and 897 mouse S-nitrosylated cysteine sites (right) were used as input for each visualization strategy. Images are scaled to the height of the largest column within the sequence visualization. The n(fg) and n(bg) values at the bottom left of the pLogo indicate the number of aligned foreground and background sequences used to generate the image, respectively. The red horizontal bars on the pLogo correspond to P = 0.05.

  2. Demonstration of the use of pLogo conditional probabilities through fixed positions.
    Figure 2: Demonstration of the use of pLogo conditional probabilities through fixed positions.

    (a) Known sites from human CaMKII substrates (n = 40 sites) were used to generate motif visualizations from the indicated tools. (b) Two residues were independently fixed in the pLogo, and these modifications reveal new pLogos in the context of the fixed positions.

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Author information

  1. These authors contributed equally to this work.

    • Joseph P O'Shea &
    • Michael F Chou

Affiliations

  1. Department of Physiology and Neurobiology, University of Connecticut, Storrs, Connecticut, USA.

    • Joseph P O'Shea,
    • Saad A Quader,
    • James K Ryan &
    • Daniel Schwartz
  2. Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA.

    • Michael F Chou &
    • George M Church

Contributions

M.F.C. and D.S. conceived of and designed the study. J.P.O., M.F.C. and D.S. gathered and analyzed the data. J.P.O. and D.S. designed the website. J.P.O., S.A.Q. and J.K.R. coded the website. G.M.C. provided materials and experimental insights. D.S. wrote the initial manuscript. All authors helped edit the final manuscript.

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The authors declare no competing financial interests.

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