Find Genomes
Genome Browser
The Genome Browser provides multiple entry points into the IMG system. You can view an alphabetical list of all genomes whose genomes are available for analysis, or you can view the list as a phylogenetic tree. Whichever listing you use, you can then click on an individual genome to view details about its genome and follow links to useful groupings of genes within that genome (e.g., genes connected to KEGG pathways). The default alphabetical list of genomes within their domains includes genome status, genome size, and sequencing center information. With the phylogenetic view, you can select or deselect all of the genomes in a particular taxon.
Figure 8. You can view the genomes alphabetically within their domains
Figure 9. You can view the genome list in a phylogenetic tree
You can sort the alphabetical listing by table columns by clicking on the column name. Alphabetical columns are usually sorted in ascending order. Numeric columns are usually sorted in descending order (most to least significant). Additionally, you can configure the table to view additional columns using the Configuration selector at the bottom of the page.
Figure 10. You can customize the genome table display
You can configure the genome table display by adding or deleting columns of data. To add a column, click the Output box next to the column name in the Configuration selector, then select the “Display Genomes Again” button.
You can save selected genomes from the table to be used as filters for other IMG analysis tools. Genomes are saved by clicking the checkmark box next to each genome, and then clicking on "Save Selections." You also have the option to “Select All” of the genomes or “Clear All” of the selections.
The genome selections you save will be used in conjunction with IMG analysis tools such as Gene Search, Gene Ortholog Neighborhoods, Phylogenetic Profiler, Genome Stats, and highlighting in ortholog and homolog lists. The box in the upper right-hand corner of the browser window displays how many genomes are selected for the current analysis tool.
Refer to the "Genome Lists and Details" section for information regarding the export of selected genome data to an Excel spreadsheet.
The summaries on the IMG home page provide quick links to subgroups of genomes that can be viewed in the Genome Browser. Click on an underlined value to load the list of genomes it represents. For example, you can quickly retrieve a list of all the bacteria that were "finished" at JGI by clicking on the first number under "JGI" in the "Bacteria" row.
Figure 11. IMG home page genome summaries
Genome Search
Genomes can be searched using several filters or by categories. Keywords or substrings are used to search names and descriptions. Genome identifier (ID) values should be exact. Searchable fields are available in the pull-down filter list, including "Genome Name," "Taxon ID," "Sequencing Status," "Sequencing Center," “Domain,” “Phylum,” and "Funding Agency."
As an example, to perform a general search of all genomes added in a particular IMG release, such as 1.2, select the “IMG Release” filter, type “1.2” in the keyword box, and click on the “Go” button. To view all genomes sequenced at JGI, select the “ Sequencing Center” filter, type “JGI” in the keyword box, and click on the “Go” button.
The list of filter options will increase in the future.
Figure 12. Genome Search
Genomes may also be searched against implicit attributes through the Quick Genome Search box at the top right corner of every IMG page.
Figure 13. Quick Genome Search
Genome Search by Categories
Genomes can also be searched using one or several of the following categories: Phenotype, Ecotype, Disease, and Relevance. Click on one or more values for each category from the scrolling lists. Categories without selected items will be ignored in the search. A logical "AND" is used when searching multiple values selected within a single category. A logical "OR" is used when searching for values across multiple categories. Once your selections have been made, click on the “Go” button to see the search results.
Figure 14. Genome Search by phenotype and ecotype
In the example, the phenotype “Acidophile” and the ecotype “Wine” are selected. The result of the search is genome Gluconobacter oxydans 621H.
Figure 15. Result of Genome Search by phenotype and ecotype