- How to show a new genome (not already available in IGB)
- For advanced users - Naming genomes and genome versions
IGB provides access to a wide variety of species and genome versions, not just the species shown on the start page. To check whether a given genome version 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.
This page will help you get started.
How to show a new genome (not already available in IGB)
Step one: Go to the IGB start screen
Go back to the IGB start screen by clicking the link labeled Species in the Current Genome tab. You can also return to the start screen by choosing 'Species' in the Species menu or use the Go to Home Page shortcut in the Toolbar.
Step two: Open your reference sequence file
Choose File > Open Reference Sequence .... and then choose the file that contains your reference genome sequence.
To load sequence bases, click Load Data.
Step three: Open annotations files
Choose File > Open to open files containing annotations. As with the reference sequence, you'll need to click Load Data to load the data into the viewer.
However, if the your reference sequence file and your annotations files don't use the same names for sequences, 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 the month and year of release combined with genus and species, following the pattern: G_species_mon_yyyy, where G is the first letter of the genus, mon is the three-letter English abbreviation for the month the genome was released, and year is the year of the release.
For example, A_thaliana_Jun_2009 is the Arabidopsis thaliana genome assembly and annotation published in June of 2009; or H_sapiens_Feb_2009 which is the Homo sapiens genome assembly published February of 2009. Using this scheme will ensure that IGB displays the latest genome first in the genome version menu under the Current Genome 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 dropbox menu to choose a species to view in IGB, a 'tool tip' appears indicating the species common name.
If you are adding a new species, contact the IGB developers and ask to have your common name added to the species.txt file under version control at sourceforge.net. This is a tab delimited file that lists all the species that IGB supports, including common names for many of them.
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.
Different groups tend to refer to the same genome version by different names.
For example, NCBI human genome build 35 is also known as hg17 and ensembl1834, as well as H_sapiens_May_2004. When IGB is able to recognize that two names refer to the same genome or chromosome, it will merge the data. Otherwise it will keep the two data sets distinct. Currently, IGB uses a simple table of synonyms to store these associations. You can create your own set of synonyms that will extend this set if needed.
These synonyms also cover the names of the chromosomes inside each of these assemblies. While some may refer to CHR1, or chr1, or chr 1, IGB can recognize that they refer to the same sequence when the synonyms files are properly updated. As a default, IGB is case-insensitive to the genome and chromosome names. The default synonyms also cover almost all genome versions up to date. If you need to add to the synonyms however, read about Personal Synonyms in the Data Sources Tab page.