BLAST against local data

Running BLAST searches on your local machine can have several advantages over running the searches remotely at the NCBI: On a technical level, the CLC Genomics Workbench uses the NCBI's blast+ software (see Thus, the results of using a particular data set to search the same database, with the same search parameters, would give the same results, whether run locally or at the NCBI.

There are a number of options for what you can search against:

To conduct a BLAST search:

   or  Toolbox | BLAST (Image blastsearch) | Local BLAST (Image blast_local)

This opens the dialog seen in figure 12.5:

Image LocalBLASTsearchstep1
Figure 12.5: Choose one or more sequences to conduct a BLAST search.

Select one or more sequences of the same type (DNA or protein) and click Next.

This opens the dialog seen in figure 12.6:

Image LocalBLASTsearchstep2
Figure 12.6: Choose a BLAST program and a target database.

At the top, you can choose between different BLAST programs. See NCBI BLAST for information about these methods.

You then specify the target database to use:

When a database or a set of sequences has been selected, click Next.

This opens the dialog seen in figure 12.7:

Image LocalBLASTsearchstep3
Figure 12.7: Examples of parameters that can be set before submitting a BLAST search.

See NCBI BLAST for information about these limitations.

There is one setting available for local BLAST jobs that is not relevant for remote searches at the NCBI: