ptm (original) (raw)
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 (Bioinformatics, 2021, btab348 ).
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:
- Brief user guide for newbies in R
- Installing ptm
- ptm Documentation
- ptm Vignettes
Last modification: 22/Feb/2021