SMC (Secondary Metabolite Collaboratory)

SMC provides a comprehensive, tool-agnostic repository of biosynthetic gene cluster (BGC) sequence data drawn from all publicly available and user-submitted bacterial and archaeal genome and contig sources to facilitate manual comparative analysis of BGC function and chemical product prediction.

Key Features:

• Searchable BGC Catalog: Users can browse a searchable catalog of putative BGCs identified from each source sequence.
• Gene and Domain Visualizations: The platform displays visualizations of gene and domain annotations derived from multiple sequence analysis tools.
• API Access: SMC's data is available through publicly-accessible application programming interface (API) endpoints to facilitate programmatic access.
• Discussion Portal: Users can share findings and search for others' findings through comment posts on BGC and source pages.

Scientific Applications:

• BGC Identification and Analysis: Researchers can identify and analyze biosynthetic gene clusters from bacterial and archaeal genomes and contigs.
• Functional Annotation of Biosynthetic Pathways: The platform supports determination of gene functions in secondary metabolite biosynthetic pathways through comparative analysis.
• Chemical Product Prediction: SMC facilitates prediction of chemical products of BGCs through careful manual comparative analysis of gene cluster data.

Methodology:

BGCs are identified from source sequences using various sequence similarity tools; gene and domain annotations are derived from multiple sequence analysis tools.