Select genomes using “magic strings”

Whenever you encounter an input box for genomes, e.g. for a BLAST search or pathway analysis, you can use magic strings to facilitate the selection of groups of genomes.

All magic strings start with an asterisk.

For example, to select all^* genomes that belong to the genus Lactobacillus, enter @taxgenus:Lactobacillus.

Alternatively, if the taxonomic class is unknown, @tax:Lactobacillus can be used to give the same result. Note: problems may arise if multiple taxonomic classes have the same name.

If certain genomes are tagged, @tag:<tag> can be used, for example @tag:anaerobe.

Examples:

• select all^* genomes: @tax:root (all NCBI taxids belong to this root taxid)
• select all^* bacterial genomes: @tax:Bacteria
• select all^* Lacticaseibacillus casei genomes: @tax:Lacticaseibacillus casei
• select all^* genomes that are tagged as anaerobe: @tag:anaerobe

(*) Important:

Magic strings only return…

• one genome per organism (the representative genome)
• non-contaminated genomes
• non-restricted genomes

Click on Show query to see the current selection of genomes.