pLogo: a probabilistic approach to visualizing sequence motifs

Joseph P O'Shea; Michael F Chou; Saad A Quader; James K Ryan; George M Church; Daniel Schwartz

doi:10.1038/nmeth.2646

pLogo: a probabilistic approach to visualizing sequence motifs

Nat Methods. 2013 Dec;10(12):1211-2. doi: 10.1038/nmeth.2646. Epub 2013 Oct 6.

Authors

Joseph P O'Shea¹, Michael F Chou, Saad A Quader, James K Ryan, George M Church, Daniel Schwartz

Affiliation

¹ 1] Department of Physiology and Neurobiology, University of Connecticut, Storrs, Connecticut, USA. [2].

PMID: 24097270
DOI: 10.1038/nmeth.2646

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.

MeSH terms

Algorithms
Amino Acid Motifs
Animals
Computational Biology / methods
Databases, Protein
Genomics
Humans
Mice
Models, Statistical
Nucleic Acids / chemistry*
Phosphorylation
Probability
Proteins / chemistry*
Proteome
Proteomics / methods
Sequence Alignment / methods*
Sequence Analysis, Protein / methods*
Software
src-Family Kinases / chemistry

Substances

Nucleic Acids
Proteins
Proteome
src-Family Kinases