PhosphoLogo is a computational tool for generating information theory-based sequence logos from a list of equal-length peptide sequences centered on the phosphorylated residues. (see PTM Centralizer.) It has been designed to be used in the context of phosphoproteomics studies, although it can be used for other post-translational modifications or position-dependent features of proteins.
PhosphoLogo has various user options including: degenerate residue grouping with choice of symbols and colors, choice of residue reference probabilities, normalization of modified residue reference probabilities, and chi-square significance filtering.
It outputs two types of information-based logos: a favored-residue logo and a disfavored-residue "anti-logo."
It also generates a relative frequency plot and chi-square p-value graph.
For more information, see Identifying Protein Kinase Target Preferences Using Mass Spectrometry by Jacqueline Douglass, Ruwan Gunaratne, Davis Bradford, Fahad Saeed, Jason D. Hoffert, Peter J. Steinbach, Mark A. Knepper, and Trairak Pisitkun. Am J Physiol Cell Physiol. 2012 Oct 1;303(7):C715-27.
To download the Java executable [.jar] file, click here.
To download a test dataset (13-aa in vitro PKA substrates), click here.
PhosphoLogo was developed by Jacqueline Douglass, Trairak Pisitkun, and Mark Knepper at the Epithelial Systems Biology Laboratory, National Heart, Lung, and Blood Institute in Bethesda, Maryland USA.
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