Contains utilities for the analysis of post-translational modifications (PTMs) in proteins, with particular emphasis on the sulfoxidation of methionine residues. Features include the ability to download, filter and analyze data from the sulfoxidation database 'MetOSite'. Utilities to search and characterize S-aromatic motifs in proteins are also provided. In addition, functions to analyze sequence environments around modifiable residues in proteins can be found. For instance, 'ptm' allows to search for amino acids either overrepresented or avoided around the modifiable residues from the proteins of interest. Functions tailored to test statistical hypothesis related to these differential sequence environments are also implemented. Further and detailed information regarding the methods in this package can be found in (Aledo (2020) < https://metositeptm.com>).
R package for the analysis of post-translational modifications, with particular emphasis on the sulfoxidation (oxidation) of methionine residues.
Extensive and detailed documentation related to this package can be found at https://metositeptm.com
Aledo, JC. ptm: an R package for the study of methionine sulfoxidation and other posttranslational modifications. Bioinformatics, Volume 37, Issue 21, 1 November 2021, Pages 3979–3980, https://doi.org/10.1093/bioinformatics/btab348
We are always interested in improving and adding additional functionality to ptm. If you have ideas, suggestions or code that your would like to distribute as part of this package, please contact us (see below).
Your are welcome to: