A-GAME

A-GAME enables end-to-end analysis of environmental DNA (eDNA) sequence data within the Galaxy framework for functional metagenomics by performing assembly, gene prediction, annotation, and candidate gene identification from pooled eDNA libraries.

Key Features:

• Comprehensive Workflow Integration: Integrates multiple bioinformatics tools and workflows within the Galaxy platform to perform end-to-end analysis from raw sequence data to candidate gene identification.
• Efficient Analysis of Pooled Libraries: Provides functionalities to process and analyze pooled eDNA libraries commonly used in functional metagenomics experiments for novel enzyme and gene discovery.
• Rapid Identification of Candidate Genes: Employs advanced assembly algorithms that outperform traditional metagenomics assemblers to accelerate and improve candidate gene identification.
• Gene Prediction and Annotation: Performs gene prediction and annotates predicted genes using integrated databases to characterize functional potential.
• Biotechnological Applications: Enables identification and characterization of novel enzymes and biologically active molecules relevant to industrial enzyme production and environmental bioremediation.

Scientific Applications:

• Functional metagenomics screening: Discovery of new microbial genes with potential industrial or environmental applications via functional metagenomics.
• Activity-based library screening: Screening eDNA libraries for active inserts based on activity assays to identify functional candidates.
• Microbial ecology and biotechnology: Characterization of the functional potential of microbial communities to support research in microbial ecology and biotechnological development.

Methodology:

Computational steps explicitly stated: upload raw sequence data; sequence assembly using advanced assembly algorithms to reconstruct genomic sequences from short reads; gene prediction and annotation using integrated databases; and candidate gene identification through combined bioinformatics analyses.