ProToDeviseR

Help :: Test dataset :: About

The Protein Topology Deviser is an R package for the automatic generation of protein topology code in JSON format. The code can be easily rendered into a graph, by Pfam's custom-domains generator. This excellent tool is not developed by us, but is embedded with the program for users' convenience. A table summary is also prepared.

This is the R package of ProToDeviseR, which can be installed locally. If you are looking for the online version of the program (which requires no installation), visit https://matrinet.shinyapps.io/ProToDeviser/.

ProToDeviseR features a fully functional graphical user interface (UI), implemented in R Shiny:

Table preview	Generated JSON code	Image generator

As an input, you can use:

• A UniProt identifier or an NCBI GenPept identifier.
• Raw results from several online resources for protein topology prediction
• A user-prepared table of protein topology annotations.

As an output, you get:

1. A table summary of protein features.
2. JSON code of protein features, ready to be pasted in the Image generator tab.

The protein features are classified as regions, motifs and markups (Figure 1). When searching with a database accession number (ID), all three are enabled by default:

• Regions: structured domains, repeats or other relatively long (usually, but not always), functional parts of the protein.
• Motifs: short liner motifs, disordered protein parts, signal peptides and transmembrane parts.
• Markups: single-amino acid targes, such as glycosylation, phosphorylation, active or binding site, etc.

Figure 1. Automatic annotation of CD45 protein topology. Identifier P08575 was searched against UniProt by ProToDeviseR. Table and JSON code were automatically generated and graphic was rendered in the Image generator tab. Regions, motifs and markups are indicated.

Dependencies and installation

ProToDeviser and its R dependencies can be installed as shown in the code box below. Depending on your system, you may need to also install system dependencies (outside R) required by them. See external Linux deps here.

# from CRAN
install.packages("jsonlite")
install.packages("seqinr")
install.packages("dplyr")
install.packages("openxlsx")
install.packages("rentrez")
install.packages("shiny")
install.packages("shinyBS")
install.packages("rclipboard")
install.packages("shinyjs")
install.packages("DT")
install.packages("textshaping")
install.packages("ragg")
install.packages("markdown")
install.packages("pkgdown")
install.packages("gggenomes")
install.packages("devtools")

# from BioConductor
install.packages("BiocManager")
BiocManager::install("IRanges")

# finally, install ProToDeviseR itself
devtools::install_github("izzilab/protodeviser")

Start up the UI

Load the library and run the UI function. To use the app graphically, that's all you need. The Help tab provides extensive documentation on the user intefrace, including examples.

library("protodeviser")
protodeviser_ui()

Functions

ProToDeviser uses the following command-line functions to generate a JSON topology scheme:

• id.JSON: for a protein database identifier (ID).
• predicted.JSON: from predicted features for your protein.
• custom.JSON: from a (manually prepared) table of features for your protein.

To generate/output features as a table:

• json.table: from JSON input of protein features.

Other places for visualization

ProToDeviser ships a modified version of the domains generator. The official custom domains generator has been decomissioned, but the Domain GFX "playground" demo is an alternative place.