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pLogo: a probabilistic approach to visualizing sequence motifs

Nature Methods volume 10, pages 1211–1212 (2013)Cite this article

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Abstract

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.

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Figure 1: Comparison of sequence logo visualizations for the pLogo, iceLogo and WebLogo tools.
Figure 2: Demonstration of the use of pLogo conditional probabilities through fixed positions.

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Acknowledgements

The authors wish to thank J. Lubner for his assistance in beta-testing the pLogo Web tool. Additionally, we thank the University of Connecticut Bioinformatics Facility for hosting the pLogo website and maintaining the server on which it runs. This study was funded in part by grants from the University of Connecticut Research Foundation (D.S.) and a Genomes to Life grant from the US Department of Energy (G.M.C.).

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Author notes

  1. Joseph P O'Shea and Michael F Chou: These authors contributed equally to this work.

Authors and 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

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  1. Joseph P O'Shea
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  2. Michael F Chou
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  3. Saad A Quader
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  5. George M Church
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  6. Daniel Schwartz
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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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Correspondence to Daniel Schwartz.

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The authors declare no competing financial interests.

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O'Shea, J., Chou, M., Quader, S. et al. pLogo: a probabilistic approach to visualizing sequence motifs. Nat Methods 10, 1211–1212 (2013). https://doi.org/10.1038/nmeth.2646

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