GRASSIUS Website Tutorial

Fasta/CSV downloads
Species and family pages include several links to export gene lists and sequences
  • Download gene list - download a table where each row represents a gene, similar to the on-screen tables on famiy pages
  • Download sequences (csv) - download a table where each row contains a transcript ID and an amino acid sequence
  • Download sequences (fasta) - download transcript IDs and amino acid sequences in fasta format

Maize Genome Versions and Translations
Grassius supports 3 version of the Maize genome:
  • Maize genome B73 RefGen_v3
  • Maize genome B73 RefGen_v4
  • Maize genome B73 RefGen_v5
When viewing Maize data, click radio buttons to select the genome version. Each genome version has a different set of gene IDs, transcript IDs, and sequences. The selected genome versions determines the primary gene ID shown in on-screen gene lists, and downloaded csv files. Downloadable sequences are different for each genome version.

Custom Family Builder
Users can create custom Maize gene families using the Custom Family Builder.

Like published families, a custom family is defined by required and forbidden protein domains. Domains are denoted by their name or pfam ID as shown on curated family pages and protein pages.

For example, family bHLH has the required domain PF00010
For example, gene ZmbHLH1 has domains PF00010 and PF14215

To use the Custom Family Builder, at least one required domain must be selected. Using the textbox under "Required Domains", start typing a domain ID such as "PF00010". Choose a domain from the auto-complete dropdown. A table of matching maize transcripts will appear. The selected domain will be given a color-code which is shown under "required" domains and in the "Domains" column in the table.

Custom families can be saved using bookmarks in your web browser. Share the url in your address bar to allow others to see your custom family. example

Copyright © 2023 | Last updated: 2023-06-26