Departamento de Biología Molecular y Bioquímica, Universidad de Málaga, Málaga 29071, Spain.
Bioinformatics. 2021 Nov 5;37(21):3979-3980. doi: 10.1093/bioinformatics/btab348.
Methionine sulfoxidation is a posttranslational modification (PTM) playing important roles in cell signaling. Herein, we present ptm, an R package for the study of this modification. However, since many of the analyses applied to methionine modification can be extended to other modifications, the package can be useful to thoroughly analyze PTMs in general. Thus, within a single software environment, ptm can integrate information from up to 11 databases covering nine modifications. Different functions can work coordinately to form pipelines allowing the programmatic analysis of thousands of proteins. Alternatively, the user can simultaneously perform different analyses on the same protein of interest, combining the results into a single output. The flexibility of ptm makes it a suitable tool to address site- and protein-centric hypotheses related to PTMs. Accompanying the package, we maintain a web page containing extended documentation and examples of the tasks that can be performed with ptm.
ptm is implemented in R. Release versions are available via CRAN and work on all major operating systems. The development version is maintained at https://bitbucket.org/jcaledo/ptm. Extended documentation can be found at https://metositeptm.com.
Supplementary data are available at Bioinformatics online.
甲硫氨酸氧化是一种在细胞信号转导中起重要作用的翻译后修饰（PTM）。在此，我们介绍了用于研究这种修饰的 R 包 ptm。然而，由于许多应用于甲硫氨酸修饰的分析方法也可以扩展到其他修饰，因此该包对于全面分析一般的 PTM 也很有用。因此，在单个软件环境中，ptm 可以整合来自涵盖 9 种修饰的多达 11 个数据库的信息。不同的功能可以协调工作，形成管道，允许对数千个蛋白质进行编程分析。或者，用户可以同时对同一感兴趣的蛋白质执行不同的分析，将结果合并到单个输出中。ptm 的灵活性使其成为解决与 PTM 相关的基于位点和基于蛋白质的假设的合适工具。该包还附带一个网页，其中包含有关可以使用 ptm 执行的任务的扩展文档和示例。
ptm 是用 R 实现的。发布版本可通过 CRAN 获取，适用于所有主要操作系统。开发版本维护在 https://bitbucket.org/jcaledo/ptm 上。扩展文档可在 https://metositeptm.com 上找到。
补充数据可在生物信息学在线获得。
