PTMoreR-enabled cross-species PTM mapping and comparative phosphoproteomics across mammals
PTMoreR (Post-translational modification ortholog aligner) is a web-based and stand-alone tool for PTM researchers and proteomics society. PTMoreR is not merely a phosphosite BLAST tool; instead, it considers the surrounding amino acid sequence of PTM sites during BLAST, enabling a motif-centric analysis across species. Additionally, PTMoreR supports a swift site-specific functional enrichment and network analysis benefiting from the well-characterized human PTM proteomic datasets. This software (online version) is available here: https://yslproteomics.shinyapps.io/PTMoreR. Please note: If the data are too large, we recommend users to intall this tool locally. Local installation can be found below.
A detailed introduction of this software can be found in the Manual.
This tool is developed with R, so if you want to run it locally, you may do some preparatory work:
1. Install R. You can download R from here: https://www.r-project.org/.
2. Install RStudio. (Recommendatory but not necessary). You can download RStudio from here: https://www.rstudio.com/.
3. Check packages. After installing R and RStudio, you should check whether you have installed these packages (shiny, shinyjs, shinyWidgets, shinyBS, shinydashboard, shinycssloaders, DT, data.table, openxlsx, Biostrings, GenomicFeatures, rtracklayer, stringi, stringr, ggsci, ggplot2, ggrepel, msa, tidyr, ggraph, graphlayouts, scales, impute, igraph, scatterpie, plotfunctions, mapplots, devtools, KinSwingR, rBLAST). You may run the codes below to check them:
if(!require(pacman)) install.packages("pacman")
pacman::p_load(shiny, shinyjs, shinyWidgets, shinyBS, shinydashboard, shinycssloaders, DT, data.table, openxlsx, Biostrings, GenomicFeatures, rtracklayer, stringi, stringr, ggsci, ggplot2, ggrepel, msa, tidyr, ggraph, graphlayouts, scales, impute, igraph, scatterpie, plotfunctions, mapplots, devtools, KinSwingR)
#Then install some packages from GitHub, as below:
devtools::install_github("drostlab/metablastr", build_vignettes = TRUE, dependencies = TRUE)
devtools::install_github("mhahsler/rBLAST")
install.packages("https://github.com/wangshisheng/motifeR/raw/master/rmotifx_1.0.tar.gz", repos = NULL, type = "source")
install.packages("https://github.com/wangshisheng/motifeR/raw/master/ggseqlogo_0.1.tar.gz", repos = NULL, type = "source")
If the preparatory work has been done, you can run this tool locally as below:
if(!require(PTMoreR)) devtools::install_github("wangshisheng/PTMoreR")
library(PTMoreR)
PTMoreR_app()
Please note, as there are many databases from different species, this package is large. If you have some issues when you install it using the code above, please try download it into your own computer and install locally. And please also feel free to write an issue or e-mail to me if you have any problem about this software.
Then PTMoreR will be started as below:
- Open PTMoreR with Chrome, Mozilla Firefox, Safari or Firefox.
- The minimum operating system specifications are: RAM 4GB, Hard drive 500 GB.
- The monitor resolution (>= 1920x1080) is better.
You could push an issue on this github. And optionally, please feel free to sent me an e-mail if you have any question or find a bug about this tool. Thank you^_^ Email: [email protected].