ProToDeviseR

ProToDeviseR generates automated protein topology schemes from database accession numbers, prediction server results, or manually prepared feature tables for proteomics studies.

Key Features:

• Automated topology generation: Generates protein topology schemes by interrogating UniProt or NCBI GenPept databases.
• Multiple input sources: Accepts database accession numbers, raw results from multiple prediction servers, or manually prepared tables of features.
• Enhanced domain rendering: Incorporates an enhanced version of Pfam's domain generator for rendering topology schemes.

Scientific Applications:

• Protein sequence characterization: Creates concise and clear protein topology schemes as part of amino acid sequence characterization in proteomics studies.
• Multi-resource data integration: Combines features from various databases and prediction servers into unified publication-ready topology schemes.

Methodology:

ProToDeviseR is implemented as an R package that queries UniProt or NCBI GenPept databases and processes input from prediction servers or manual feature tables to generate topology schemes using an enhanced version of Pfam's domain generator.