ProToDeviseR: an automated protein topology scheme generator

Abstract

Background

Amino acid sequence characterization is a fundamental part of virtually any protein analysis, and creating concise and clear protein topology schemes is of high importance in proteomics studies. Although numerous databases and prediction servers exist, it is challenging to incorporate data from various, and sometimes contending, resources into a publication-ready scheme.

Results

Here, we present the Protein Topology Deviser R package (ProToDeviseR) for the automatic generation of protein topology schemes from database accession numbers, raw results from multiple prediction servers, or a manually prepared table of features. The application offers a graphical user interface, implemented in R Shiny, hosting an enhanced version of Pfam’s domains generator for the rendering of visually appealing schemes.

Conclusions

ProToDeviseR can easily and quickly generate topology schemes by interrogating UniProt or NCBI GenPept databases and elegantly combine features from various resources.