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, 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 local BLAST search, go to:

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

This opens the dialog seen in figure 16.5:

Image LocalBLASTsearchstep1
Figure 16.5: 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 16.6:

Image LocalBLASTsearchstep2
Figure 16.6: Choose a BLAST program and a target database.

At the top, you can choose between different BLAST programs.

BLAST programs for DNA query sequences:

BLAST programs for protein query sequences:

In cases where you have selected blastx or tblastx to conduct a search, you will get the option of selecting a translation table for the genetic code. The standard genetic code is set as default. This setting is particularly useful when working with organisms or organelles that have a genetic code that differs from the standard genetic code.

If you search against the Protein Data Bank database and homologous sequences are found to the query sequence, these can be downloaded and opened with the 3D Molecule Viewer (see BLAST search against the PDB database).

You then specify the target database to use:

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

The next dialog allows you to adjust the parameters to meet the requirements of your BLAST search (figure 16.7).

Image BLAST_Local_parameters
Figure 16.7: Parameters that can be set before submitting a local BLAST search.

BLAST a partial sequence against a local database

You can search a database using only a part of a sequence directly from the sequence view:

        select the region that you wish to BLAST | right-click the selection | BLAST Selection Against Local Database (Image blast_local)

This will go directly to the dialog shown in figure 16.6 and the rest of the options are the same as when performing a BLAST search with a full sequence.