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CHAPTER 12. BLAST SEARCH
12.1.1
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BLAST at NCBI
When running a BLAST search at the NCBI, the Workbench sends the sequences you select to
the NCBI's BLAST servers. When the results are ready, they will be automatically downloaded
and displayed in the Workbench. When you enter a large number of sequences for searching with
BLAST, the Workbench automatically splits the sequences up into smaller subsets and sends
one subset at the time to NCBI. This is to avoid exceeding any internal limits the NCBI places on
the number of sequences that can be submitted to them for BLAST searching. The size of the
subset created in the CLC software depends both on the number and size of the sequences.
To start a BLAST job to search your sequences against databases held at the NCBI:
Toolbox | BLAST (
) | NCBI BLAST (
)
Alternatively, use the keyboard shortcut: Ctrl+Shift+B for Windows and
+Shift+B on Mac OS.
This opens the dialog seen in figure 12.2
Figure 12.2: Choose one or more sequences to conduct a BLAST search with.
Select one or more sequences of the same type (either DNA or protein) and click Next.
In this dialog, you choose which type of BLAST search to conduct, and which database to search
against. See figure 12.3. The databases at the NCBI listed in the dropdown box will correspond
to the query sequence type you have, DNA or protein, and the type of blast search you have
chosen to run. A complete list of these databases can be found in Appendix D. Here you can also
read how to add additional databases available the NCBI to the list provided in the dropdown
menu.
Figure 12.3: Choose a BLAST Program and a database for the search.
BLAST programs for DNA query sequences: