IGB User's Guide
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Introduction

IGB already supports many species and genome versions, not just the species shown on the start screen. To check whether a genome is available in IGB, click the Current Sequence tab and use the Species and Genome Version menus to look for your genome of interest.

However, if your genome is not available, you can still use IGB. Here's how:

How to show a custom genome in IGB

  1. Return to the IGB Start Screen. To return to the start screen, click the Home icon in the Toolbar. You can also select "Species" in the Species menu in the Current Genome tab.
  2. Select File > Custom Genome to open the Custom Genome window
  3. Enter a species name and genome version name.
  4. Select a reference sequence file. 
  5. Click OK.

 

Viewing reference gene model annotations

If you have annotations for your genome, use File > Open File... to open and view them in IGB.

 

Note: The sequence names in your gene models file and reference sequence file need to match. If they don't, then you can create a chromosome synonyms file that IGB will use to match names.

For advanced users - Naming genomes and genome versions

Naming a Genome

If you are building a genome for display in IGB, we recommend that you give it an IGB-friendly name, consisting of a genus and species prefix combined with the month and year of release, following the pattern:

G_species_MMM_YYYY

where

  • G is the first letter of the genus
  • species is the species name
  • MMM is the three-letter English abbreviation for the month the genome was released
  • YYYY is the year of the release.

For example, A_thaliana_Jun_2009 is the Arabidopsis thaliana genome assembly released June of 2009.

Using IGB-friendly names ensures that IGB displays the latest genome first in the Genome Version menu in the Current Genome tabbed panel.

If you are working with a subspecies or strain, you can also include the subspecies name.

For example, if you are working with Helicobacter pylori 26695 (released July 2012) then enter species Helicobacter pylori 26695 and genome version H_pylori_26695_Jul_2012.

Adding a Common Name for a Species

When users operate the Species menu, a tooltip appears that lists the species common name. This information comes from a file named species.txt that is packaged with IGB application.

If you are adding a new species, contact the IGB developers and ask to have your common name added to the species.txt file.  

If you are distributing your own data sets via a QuickLoad site, you can also place your own custom species.txt file in the root directory of the QuickLoad site.

For more information, see: Sharing data for a custom genome not already part of IGB QuickLoad and Matching species and genome versions.

 

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