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BioCyc.org is an extensive web portal containing 19,000 genomes and associated metabolic pathways for microbes, model eukaryotes, and humans. The BioCyc website provides extensive bioinformatics tools for searching and analyzing these databases, and leveraging them for analysis of omics datasets. The Medical Library provides free access to BioCyc (create your account here)  

Topics include: 

• Database selection
• Search operations
• Gene, metabolite, reaction, and pathway pages
• BLAST search, sequence pattern search, extracting sequences
• Regulation in BioCyc
• Update notifications

BioCyc.org is an extensive web portal containing 19,000 genomes and associated metabolic pathways for microbes, model eukaryotes, and humans. The BioCyc website provides extensive bioinformatics tools for searching and analyzing these databases, and leveraging them for analysis of omics datasets. 

BioCyc databases combine curated information with data imported from multiple sources, and with computationally inferred data (metabolic pathways, operons, PFam domains, and orthologs). Curated databases receive intensive review and updating by a Ph.D. biologist that includes reviewing the computationally predicted metabolic pathways, entering new gene functions and metabolic pathways from the experimental literature, defining regulatory relationships, and creating protein complexes. Overall the BioCyc databases have been curated from 130,000 publications. 

BioCyc genome-related tools include a genome browser, sequence searching and alignment, and extraction of sequence regions. Pathway-related tools include pathway diagrams, a tool for navigating zoomable organism-specific metabolic map diagrams, and a tool for searching for metabolic routes that transform a starting metabolite into a product metabolite. Regulation tools depict operons and regulatory sites, as well as showing full organism regulatory networks. Comparative analysis tools enable comparisons of genome organization, of orthologs, and of pathway complements. Omics data analysis tools support enrichment analysis and painting of transcriptomics and metabolomics data onto individual pathway diagrams and onto zoomable metabolic map diagrams. The Omics Dashboard tool enables interactive exploration of omics datasets through a hierachy of cellular systems.