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Basic Help for BioCyc

How to Search BioCyc

The first step in querying BioCyc is to select the database you wish to query. You can select a database in two places:

  • Click on the words change organism database under the "Quick Search" box in the upper right corner
  • Click on the words change organism database at the bottom of the toolbar Search menu or Tools menu

The BioCyc Web site provides a variety of search tools to help you find the information you are looking for.

  • Search by words and database fields: All BioCyc databases, such as EcoCyc, provide three layers of searches.

    • Quick Search: Enter one or more words or text fragments in the box to the upper right of the toolbar and click Search. [more details]

    • Search by single object type from Toolbar Search menu [more details].
      These searches allow filtering on multiple attributes of a single type of object. Examples:
      • Search Menu → Genes/Proteins/RNAs
      • Search Menu → Pathways

    • Advanced searches: Search Menu → Advanced [more details]
      These searches allow very sophisticated filtering on attributes and relationships of multiple object types.

  • Search by ontology: See Search Menu → Ontologies [more details]

  • BLAST search: See Search Menu → BLAST [more details]

  • Search BioCyc Web pages: See Search Menu → Google this Site [more details]

  • Search the full text of the E. coli literature: See Search Menu → Search Full-text Articles [more details]

How to Learn More

For more information see:

  • The Website User Guide under the Help menu in the top menu bar

  • The online BioCyc Webinars

BioCyc Tools

Please explore the Genome, Metabolism, and Analysis menus, which offer a variety of software tools including visualization of genome maps, metabolic networks, and regulatory networks; multiple tools for analysis of omics data; and comparative analyses and reports.

Right Operations Menu

At the right side of pages such as gene, metabolite, and pathway pages, is the right-operations menu. The menu offers commands for operating on the currently displayed object, e.g., for showing the current gene within a comparative genome browser, or for customizing the appearance of the current pathway. The contents of this menu change depending on the type of object currently displayed.

What to Bookmark

We suggest you bookmark some or all of these pages in your Web browser, depending on which databases you use most frequently.

What Web Browser to Use with the BioCyc Web Site

We suggest you use the following Web browsers:
  • Firefox version 2 or higher
  • Chrome version 5 or higher

Less recommended:

  • Safari version 3 or higher
    • Will not display atom mappings on reaction pages
    • Does not support metabolic route search
  • Internet Explorer version 10 or higher
    • Will not display atom mappings on reaction pages
    • Does not support metabolic route search

Sending Problem Reports and Suggestions

Please report Web site problems and errors or omissions in BioCyc databases, as well as general suggestions, as follows.

  • Click on "Report Errors or Provide Feedback" at the bottom of most data pages
  • Email a bug report or suggestion to . Please be clear about which Web page you are referring to; inclusion of a URL in your report is very helpful.