BLAST sequence similarity searching

What is BLAST?

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. This can help with tasks such as finding homologous proteins and determining protein function.

How to use BLAST

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 49). You can submit multiple sequences at a time, up to a maximum of 5 sequences, in which case a job will be created in your dashboard for each of the sequences.
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 you are interested in. For example, ‘Homo sapiens [9606]’ enables you to restrict the search to human entries while using ‘Mammalia [40674]’ will extend it to include all mammals. An auto-complete functionality will help you with this.
5. If you are running multiple jobs and need to identify each one, you can name the job but this is optional. By default, the job name is auto-generated based on the submitted sequences. Job identifiers and the related data are kept for seven days and are then deleted.
6. 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.
7. Click the ‘Run Blast’ button.

BLAST searches can also be run directly in UniProt entry pages by selecting BLAST in the ‘Tools’ dropdown menu. 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’. 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.

Supported identifiers

Supported UniProt identifiers include: