Brownotate

Brownotate generates protein sequence databases for any species from available sequencing information.

Key Features:

• Protein sequence extraction: Extracts already existing protein sequences from available data.
• Genome assembly annotation: Automatically annotates any genome assembly to generate protein sequences.
• De novo assembly and annotation: Assembles and annotates any DNA sequence dataset to generate protein sequences.

Scientific Applications:

• Proteomics database generation: Generates protein sequence databases for species lacking existing databases to enable proteomic analysis.
• Cross-species proteomics: Supports proteomic data interpretation across diverse species from prokaryotes to eukaryotes.
• Sequencing data utilization: Enables immediate proteomic analysis of samples from species with only sequencing data available.

Methodology:

The pipeline extracts existing protein sequences, or automatically annotates genome assemblies, or assembles and annotates DNA sequence datasets. Performance was evaluated by comparing assembly fragmentation and completeness against evolutionary expectations of gene content, and by comparing proteomics data interpretation against NCBI reference databases using PRIDE repository data for 27 species.