Microbial Genomes Web Portal
Curated Data Derived from over 65,000 Publications
Genome Informatics and Comparative Genomics Tools
Omics Data Analysis Tools
Quantitative Metabolic Models
Advanced Database Access
The BioCyc web portal from SRI International contains 10,000 Pathway/Genome Databases (PGDB). Each BioCyc PGDB describes the genome of an organism, as well as its biochemical pathways and, for a small fraction of organisms, its regulatory network.
Manually Curated Databases
Computationally Generated Databases with some Manual Curation
Computationally Generated Databases
All PGDBs include the genome, predicted metabolic pathways, and predicted pathway hole ﬁllers (genes coding for missing enzymes in metabolic pathways). Bacterial PGDBs include predicted operons. The exact types of data present in different databases will vary. Many databases also include:
A Sample of the Most Popular BioCyc Informatics Tools:
BioCyc curators summarize and synthesize information from thousands of publications, saving scientists time in literature research, and integrating data for large-scale computational analyses.
BioCyc provides a powerful and comprehensive set of features for querying, visualization, and analysis of BioCyc data and user data. Some of our more popular tools are listed here.
Genome browser depiction of a region of the E. coli chromosome.
Gene colors indicate operon organization. Promoters and terminators are depicted when known. Pseudogenes are marked with X’s.
The Regulatory Overview depicts the transcriptional regulatory network in a PGDB. Here, the E. coli regulatory network is highlighted to show genes that regulate the gntR gene (blue lines), and the genes that are regulated by gntR (purple lines). The inner two rings are populated by transcription factors and sigma factors; the outer ring contains other genes.
Genome browser with tracks display enabled. The single track shown here was generated from a data file containing ChIP-chip data for RNA polymerase binding. This facility allows the user
to compare the frequency of protein binding from ChIP-chip experiments against curated promoters within a PGDB.
Cellular Omics Viewer enables the user to paint omics datasets onto the Cellular Overview diagram. Scientists can interpret gene expression, proteomics, and metabolomics datasets in a pathway context, including animation of time-course or comparative datasets.
The Cellular Omics viewer paints omics datasets onto a diagram of the cellular biochemical network. Reaction lines can be colored with gene expression, proteomics, or reaction flux data; compound nodes can be colored with metabolomics data. Multi-omics data can be analyzed by coloring data onto reactions and metabolites simultaneously. Omics pop-ups graph omics data values using bar graphs, heat maps, or X-Y plots.
(above) Output from the RouteSearch tool for metabolic path searching. The tool was asked to find paths from aldehyde-D-xylose to ethylene glycol in E. coli. The two lowest-cost paths are shown; the second path is truncated. Coloring of the chemical structures indicates conservation of atoms along the pathways. Red arrows indicate reactions added from MetaCyc.
For information on BioCyc subscriptions please view the Subscriptions tab above.
The BioCyc web portal from SRI International contains genome and metabolic-pathway information for over 10,000 microbes. BioCyc encyclopedias are unique in integrating a diverse range of data and providing a high level of curation for important microbes. BioCyc curators summarize and synthesize information from thousands of publications, saving scientists time in literature research, and integrating data for large-scale computational analyses.
BioCyc Pathway/Genome Databases (PGDB) describe the genome of an organism, as well as its biochemical pathways and (for a small fraction of organisms) its regulatory network. New releases occur three times per year, often including new databases as well as updated data. Two members of the BioCyc collection, the EcoCyc and MetaCyc databases, are derived from more than three decades of literature-based curation of genome and pathway data. The HumanCyc database provides a curated collection of many human metabolic pathways and enzymes.
BioCyc bioinformatics tools combine unparalleled breadth and user friendliness and include a unique set of visualization tools to speed comprehension of its extensive and complex data. For a full list of analysis and visualization tools please refer to the BioCyc Data Sheet.