Package: ptm 1.0.1
ptm: Analyses of Protein Post-Translational Modifications
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>).
Authors:
ptm_1.0.1.tar.gz
ptm_1.0.1.zip(r-4.5)ptm_1.0.1.zip(r-4.4)ptm_1.0.1.zip(r-4.3)
ptm_1.0.1.tgz(r-4.4-any)ptm_1.0.1.tgz(r-4.3-any)
ptm_1.0.1.tar.gz(r-4.5-noble)ptm_1.0.1.tar.gz(r-4.4-noble)
ptm_1.0.1.tgz(r-4.4-emscripten)ptm_1.0.1.tgz(r-4.3-emscripten)
ptm.pdf |ptm.html✨
ptm/json (API)
NEWS
| # Install 'ptm' in R: |
| install.packages('ptm', repos = c('https://jcaledo.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://bitbucket.org/jcaledo/ptm
- hmeto - Human MetO sites oxidized by hydrogen peroxide treatment.
Last updated 6 months agofrom:d9386eb060. Checks:OK: 7. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Nov 19 2024 |
| R-4.5-win | OK | Nov 19 2024 |
| R-4.5-linux | OK | Nov 19 2024 |
| R-4.4-win | OK | Nov 19 2024 |
| R-4.4-mac | OK | Nov 19 2024 |
| R-4.3-win | OK | Nov 19 2024 |
| R-4.3-mac | OK | Nov 19 2024 |
Exports:aa.ataa.compget.seqgracefully_failis.atmeto.listmeto.scanmeto.searchpairwise.distsaro.distsaro.geometrysaro.motifxprod
Dependencies:askpassbio3dcurlhttrjsonlitemimeopensslR6Rcppsys
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Find Full Paths to Executables | .get.exepath |
| Get Web Resource | .get.url |
| Residue Found at the Requested Position | aa.at |
| Amino Acid Composition | aa.comp |
| Import a Protein Sequence from a Database | get.seq |
| Check that Internet Resource Work Properly and Fail Gracefully When Not | gracefully_fail |
| Human MetO sites oxidized by hydrogen peroxide treatment. | hmeto |
| Check Residue a Fixed Position | is.at |
| List Proteins Found in MetOSite Matching a Keyword | meto.list |
| Scans a Protein in Search of MetO Sites | meto.scan |
| Search for Specific MetO Sites | meto.search |
| Compute Euclidean Distances | pairwise.dist |
| Compute Distances to the Closest Aromatic Residues | saro.dist |
| Compute Geometric Parameters of S-Aromatic Motifs | saro.geometry |
| Search for S-Aromatic Motifs | saro.motif |
| Compute Cross Product | xprod |
