BLAST sequence similarity searching

BLAST (basic local alignment search tool) is a tool for comparing primary biological sequence information such as the amino-acid sequences of proteins. A BLAST search enables a researcher to compare a subject protein (called a query) with a database of sequences, and identify database sequences that resemble the query sequence above a certain threshold.

1. Select the ‘Blast’ tab of the toolbar at the top of the page to run a sequence similarity search with the Blast program.
2. Enter either a protein or nucleotide sequence or a UniProt identifier into the form field (Figure 38 – interactive image).
3. Select your target database. The default is to search against all the reference proteomes + UniProtKB/Swiss-Prot but you may choose to just run against the reviewed sequences in UniProtKB/Swiss-Prot.
4. Restrict the species. This is optional but enables you to restrict the search species to the organism or taxonomic group or organism you are interested in. For example, ‘9606’ enables you to restrict the search to human entries, using ‘Mammalia [40674]’ will extend it to include all mammals. An auto-complete functionality will help you with this.
5. Name the job, if you are running multiple jobs and need to identify each one. This is optional.
6. Click the ‘Run Blast’ button.

Figure 38 Figure 38 The Blast input page (interactive image).

Blast searches can be run directly from the ‘Blast’ button in UniProt entry pages. All relevant results pages (such as UniProtKB, UniRef, UniParc and tool results) allow you to run a Blast search directly by selecting an entry using a checkbox. You can also run Blast searches from within the ‘Basket’.

The following kinds of UniProt identifiers are supported:

If you select the ‘Blast’ tab of the toolbar from a UniProtKB, UniRef or UniParc entry page, the current sequence is prefilled in the form.

Jobs have unique identifiers, which (depending on the job type) can be used in queries (e.g. to get the intersection of two sequence similarity searches). Job identifiers and the related data are kept for seven days, and are then deleted.

Optional settings

Advanced users may wish to change the default parameters to optimise their search. A list of optional settings for your Blast search can be found in the help section.