PomBase Documentation

PomBase Web Site Help & Documentation

Gene Pages

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How to Cite PomBase

File Formats for Data Submission

PomBase accepts batch submissions of certain types of data that appear on PomBase gene pages. For these data types, we use dedicated PomBase-specific formats:

For data that can be connected with sequence features or coordinates, and displayed as tracks in the genome browser, see the data format FAQ and further details linked there.

Linking to and from PomBase

  • Linking to PomBase: To link to any PomBase gene page, use the systematic ID for the gene in a URL with the syntax http://www.pombase.org/spombe/result/[systematic ID]. For example, http://www.pombase.org/spombe/result/SPBC11B10.09 links to the gene page for cdc2.
  • Linking from PomBase to external resources: We can provide links from PomBase gene pages to gene- or gene product-specific S. pombe data for any resource that uses URLs with PomBase systematic IDs . Please contact the PomBase Curators (web form) for more information.

 

PomBase Genome Browser Help & Documentation

  1. Configuring the browser display: See FAQs under the Genome Browser heading. The video on "The Ensembl Genome Browser: an overview" in the Ensembl Tutorials collection may also be useful.
  2. Displaying your own data: Adding Custom Tracks (includes links to file format documentation)

Comparative Genomics

We plan to add specific documentation about comparative genomics using S. pombe here. In the meantime, you can look at the documentation for Ensembl Compara.

About Ensembl Genomes

S. pombe is included in Ensembl Fungi, which is part of Ensembl Genomes. You can explore the project starting from the Ensembl Genomes home page.

Technical Information and Assistance

Links to Ensembl Genomes pages that may be of interest to programmers, bioinformaticians, and other technically inclined users

  1. The Ensembl Genomes Perl API
  2. Doxygen Perl module documentation for the Ensembl code base
  3. Ensembl Genomes Distributed Annotation System (DAS) documentation
  4. Installing Ensembl Genomes webcode
  5. Known Ensembl Bugs
  6. Ensembl software licence and legal notices

More information ...

Additional PomBase documentation and help will be available here soon. In the meantime, you can contact the PomBase Curators (web form)