BioCyc Microbial Genomes and Metabolic Pathways Web Portal

BioCyc Database Collection Logo

 

 

 

The BioCyc Microbial Genomes and Metabolic Pathways Web Portal is coming to the University of Cincinnati.

Beginning August 31st, researchers can access the full suite of databases in the BioCyc Database Collection. 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 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. 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.

BioCyc databases integrate extensive data for each organism, and provide platforms for analysis of large-scale datasets. BioCyc enables scientists to pursue several use cases:

  • BioCyc is a massive encyclopedic reference on microbial genes, metabolites, and pathways that integrates information from many sources. Scientists consult BioCyc to save large amounts of time finding, understanding, and synthesizing material from the primary literature.
  • BioCyc is a genome informatics and comparative genomics platform.
  • BioCyc enables exploration of a vast set of biological networks.
  • BioCyc provides gene-expression, metabolomics, and multi-omics analysis tools.
  • BioCyc provides executable metabolic models for a small but growing set of organisms.

BioCyc Informatics Tools

  • Search for genomes by name, taxonomy, phenotypic properties.
  • Gene information page
    • Retrieve amino-acid sequence and nucleotide sequence of arbitrary genome region.
    • Query genes by gene name, accession number, sequence length, replicon position, protein properties (pI, MW, protein features, subcellular location, ligand), GO terms.
  • Transcription-unit information page.
  • Genome Browser depicts genomic regions at user-selected resolution with semantic zooming that reveals new features at higher resolutions. Visible features include pseudogenes, promoters, transcription-factor binding sites, repeats, terminators, nucleotide sequence. Zoom to sequence. Generate genome poster.
  • BLAST search sequence-pattern search via patmatchMap SNPs to genes and show effects on translation.

Access this URL for more information about BioCyc databases and features: https://biocyc.org/intro.shtml.

Some additional links that may be helpful:

Webinars: https://biocyc.org/webinar.shtml

Guided tour: https://biocyc.org/samples.shtml

User guide: https://biocyc.org/PToolsWebsiteHowto.shtml

Data Sheet: BioCyc data sheet

Questions?

Contact:

Tiffany J. Grant, PhD
Interim, Assistant Director for Research and Informatics
Research Informationist
Co-Leader, Research Services
Health Sciences Library
Office: (513) 558-9153
E-mail: joffritm@ucmail.uc.edu
Web: http://libraries.uc.edu/digital-scholarship/data-services.html

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