Extensive, Highly Curated Data
BioCyc integrates genome data with a comprehensive body of additional data including metabolic reconstructions, regulatory networks, protein features, orthologs, gene essentiality, and atom mappings.
A Vast Set of Bioinformatics Tools
Browsers for genomes, metabolic networks, and regulatory networks. Transcriptomics and metabolomics data analysis, comparative analysis, and metabolic route search. Sequence search and alignment.
Explore Metabolic Maps for Thousands of Organisms
The Cellular Overview enables you to browse through zoomable metabolic map diagrams that are customized to each BioCyc organism.
Clostridioides difficile on your iPhone and iPad
Have you ever wanted to quickly find out what is known about a gene, protein or pathway that was just mentioned in a talk or on a poster? Download the free BioCyc iPhone app to browse BioCyc on the go! Try the iPad version as well.
RouteSearch: Search for Paths Through the Metabolic Network
Search for lowest-cost paths through the metabolic network of the selected organism.
Metabolic Reconstruction from Sequenced Genomes
Install SRI's Pathway Tools software (free to academics) to predict metabolic pathways for sequenced genomes, generate metabolic models.
Gene Expression Data Analysis
Multiple tools are available in this website for analysis of gene expression data.
Comparative Genome Analysis
Multiple comparative analysis tools are available in this website.
Search Databases by Organism Properties
BioCyc contains data on phenotypic properties of organisms, such as human-microbiome body site, aerobicity, and temperature range.
The BioCyc Database Collection
Tier 1 databases such as EcoCyc are the most highly curated. BioCyc databases are computationally derived from MetaCyc.Request Addition of New Genome to BioCyc
The Omics Dashboard: A New View of Omics Data
Visualize omics data as a set of graphs hierarchically organized by functional category. Drill down for more detail in areas of interest.
Clostridioides difficile Pathway/Genome Databases
Clostridioides difficile infections are a growing public health threat. Use of broad-spectrum antibiotics in health care settings can disrupt the normal gut microbiota and allow C. difficile to thrive. Current treatment options are limited and include additional courses of antibiotics, surgical removal of the colon, and fecal transplants.
This website contains 16 Clostridioides difficile genomes (show list) and associated metabolic pathways. This site is part of the larger BioCyc collection of thousands of Pathway/Genome Databases for sequenced genomes. Click the "Change Current Database" button (above) to explore the available databases.
This site includes extensive retrieval, visualization and analysis tools, including a genome browser and a metabolic map diagram. There are tools for analysis of gene expression, metabolomics and ChIP-chip data. You can search and align sequences for Vibrio cholerae and other microbial genomes and perform comparative analysis. You can store groups of genes and pathways into a SmartTable, and then browse, analyze and share with other users.
What people are saying
"BsubCyc is a tool of the utmost value."
Prof. of Biochemistry
& Molecular Biology
"My lab uses these resources on a daily basis."
Professor and Chair,
Dep't. of Biomolecular Chemistry
"We rely on BioCyc's Gene Pages and Overview Diagrams almost daily."
Assoc. Prof. Biochemistry
"We use BioCyc and MetaCyc extensively to investigate the metabolic and regulatory processes of organisms we study."
William Cannon, Team Lead
"BioCyc is the go-to resource of knowledge and tools for Ginkgo scientists."
"BioCyc is a tremendous resource for pathway analysis in metabolomics."
Art Edison, Dept of Genetics
"We make extensive use of the BioCyc full metabolic network diagram for omics data analysis."
Timothy J. Donohue, Director
"I have not found another database that has a better interface than BioCyc."
Gary B. Huffnagle, Professor
Microbiology and Immunology
Tutorial #1: Introduction to BioCyc
Tutorial #2: Introduction to SmartTables
Tutorial #3: Zoomable Metabolic Map, Comparative Tools, Regulatory Network
Tutorial #4: Omics Data Analysis
Tutorial #5: Pathway Collages
Tutorial #6: Creating a Pathway/Genome Database
- Part 1A: Introduction to Database Building and Pathologic (14:04)
- Part 1B: Building a Database: Detailed Pathologic Example (23:53)
- Part 2A: General Editing Strategies (8:00)
- Part 2B: Creating and Editing Reactions and Compounds (17:32)
- Part 2C: Updating Proteins, Citations, GO Terms, and Enzymatic Reactions (26:10)
- Part 2D: Making and Editing Pathways (9:42)