Overview

ptm is an R package containing utilities for the analysis of post-translational modifications (PTMs) in proteins, with particular emphasis on the sulfoxidation of methionine residues.

It is currently distributed as platform independent source code under the GPL version 2 license. Please, see the Installing ptm page for installation instructions.

Features

  • Straigthforward way to download, filter and analyze data from the sulfoxidation database MetOSite.
  • Integration of major protein PTM and sequence databases and associated search tools.
  • Data visualization: by using visual elements like charts, graphs, and maps, data visualization tools provide an accessible way to see and understand trends, outliers, and patterns in data related to PTM.
  • In addition, various utility functions are provided to enable the statistical and graphical power of the R environment to work with biological sequence and structural data.

Development

For information on current and future development of ptm, see the ptm project on BitBucket.

Citing ptm

  • ptm: an R package for the study of methionine sulfoxidation and other post-translational modifications (manuscript under revision).

Other related works

  • MetOSite: an integrated resource for the study of methionine residues sulfoxidation, Bioinformatics, 2019, 35:4849–4850.
    (Abstract | PubMed)
  • Methionine in proteins: The Cinderella of the proteinogenic amino acids, Protein Sci., 2019, 28:1785-1796.
    (Abstract | PubMed)

What’s next

Depending on your degree of familiarity with R, you can choose between:

Last modification: 22/Feb/2021