FunGeCo

FunGeCo integrates gene context and homology information to improve functional inference of microbial genomes and metagenomes by distinguishing cognate homologs and refining pathway-specific assignments.

Key Features:

• Gene context-based functional inference: Integrates gene context information with homology to distinguish cognate homologs and refine pathway-specific functional predictions.
• Literature mining and manual curation: Combines literature mining with manual curation to generate gene context-based modules for annotation.
• Comparative genomic analysis: Performs comparative analyses of genomes against those available in NCBI databases.
• Synteny and genomic visualizations: Provides synteny views using parallel coordinates and circular genomic representations and supports comparison of up to five genomes.
• Tabular outputs for detailed analysis: Produces tabular outputs detailing module presence and attributes across genomes.

Scientific Applications:

• Microbial ecology and environmental microbiology: Infers functional potential of resident microbes within environmental samples to support ecological studies.
• Genomic research and annotation: Supports annotation of newly sequenced genomes with gene context-based functional assignments.
• Comparative genomics: Enables analysis of evolutionary relationships and functional conservation among microbial species through comparative analyses and synteny visualization.

Methodology:

Integration of homology-based information with gene context data; literature mining and manual curation to create gene context modules; comparative genomic analyses against genomes in NCBI databases; synteny analysis using parallel coordinates and circular genomic representations; and generation of tabular module outputs.