StandEnA

StandEnA generates customizable standardized protein annotation databases and presence-absence matrices by retrieving protein sequences and synonyms from multiple public databases based on user-defined standard names to support prokaryotic genome and metagenome comparative analyses.

Key Features:

• Custom Database Generation: Retrieves protein sequences from multiple public databases based on a user-defined list of standard names and compiles them into a custom database.
• Synonym Mapping: Searches for and collects synonyms corresponding to standard names across selected public databases to expand annotation coverage.
• Standardization and Comparability: Produces standardized annotation outputs and reference files containing standard database identifiers to enable comparability across datasets.
• Presence-Absence Matrix Creation: Generates presence-absence matrices from annotated genomes for comparative analyses of protein presence across samples or conditions.
• Reference File Generation: Compiles standardized reference files that map standard names to database identifiers for downstream analyses.

Scientific Applications:

• Prokaryotic Genome Annotation: Supports annotation workflows for prokaryotic genomes by providing custom databases and standardized identifiers.
• Comparative Genomics and Metagenomics: Enables comparative analyses using presence-absence matrices to identify protein distribution across genomes or metagenome-assembled genomes.
• Cross-study Standardization: Provides standardized reference files to facilitate consistent data representation and interpretation across studies.
• Demonstrated Use Case: Applied to six metagenome-assembled genomes to analyze three distinct biological pathways.

Methodology:

Users define a list of standard names; StandEnA retrieves corresponding protein sequences and synonyms from selected public databases and compiles them into a custom database, which is then used for genome annotation and generation of presence-absence matrices and standardized reference files.