OrtSuite

OrtSuite identifies orthologous gene clusters and annotates microbial genomes to detect user-defined functions and infer potential microbial interactions in ecosystem processes.

Key Features:

• Ortholog clustering and genome annotation: Combines ortholog clustering with genome annotation to detect genes associated with user-defined functions.
• Functional annotation using a user-curated database: Leverages a user-curated database to assign functions to genes and support hypothesis-driven analyses.
• Validation and accuracy: In validation studies, matched 96% of experimentally verified KEGG orthologs involved in benzoate degradation within a known group of degraders.
• Synergistic species interaction identification: Evaluated for identifying putative synergistic species interactions using sequenced genomes from independent studies, including cases of benzoate degradation.
• Extensibility and customization: Applicable to other ecosystem processes where gene-reaction connections are established.

Scientific Applications:

• Microbial interaction prediction: Infers putative synergistic interactions among microbial species from genome content.
• Ecosystem process targeting: Enables focused analysis of specific ecological processes such as benzoate degradation and other nutrient or pollutant transformations.
• Hypothesis-driven research: Supports targeted testing of gene-function associations using curated functional data.

Methodology:

Integrates ortholog clustering with genome annotation, uses a user-curated database to assign functions based on user-defined targets, analyzes sequenced genomes to identify putative synergistic interactions, and validates assignments by comparison to experimentally verified KEGG orthologs (e.g., benzoate degradation).