Sequences and BLAST searching

You can conduct a BLAST search from within MultiSeq if you have the BLAST program installed on your computer. You will need to install and configure BLAST if you haven't already done so (see 1.2.1).

1. Before you open the Import data window, you have the option of either selecting a set of sequences by ctrl/shift clicking sequence titles, or a region within a sequence by clicking within the sequences themselves.
2. Go to File and then Import data and select From BLAST Search, and either All Sequences, Marked Sequences, or Selected Regions (see 3.6).
3. In the Databases dialog, either type the location of the database, or use the Browse button to locate it. This could be something like a Swiss PROT database or otherwise. Once you give MultiSeq the name of a database, it will remember it for future searches.
4. Select the E Score, Iterations, and Max Results.
5. If you want MultiSeq to automatically download structure information for sequences found via the BLAST search, mark the checkbox for that.
6. Click the OK button.

Figure 5: BLAST Search Results

MultiSeq will then begin a BLAST search. This may take several minutes. When the search is done, a new window called BLAST Search Results will appear. The results do not immediately appear in the main MultiSeq window, because you can apply further filters on the retrieved sequences. The BLAST Search Results window is divided into three main parts: the sequence viewer, Filter Options, and View Options (see Fig. 5).

The sequence viewer is a read-only display of the sequences that match your BLAST search. The number of matches is listed below the sequence viewer.

You can use the Zoom to change how much of each sequence you see. You can change the zoom level and Apply View and you will see fewer or more sequences in the sequence viewer portion of the window.

In the Filter Options you can tweak the parameters to reduce or expand the number of sequence matches. Once you have changed a parameter you can hit Apply Filter and see which sequences match.

Once you have a collection of sequences that you want to import, you can hit the Accept button at the bottom and they will be added to the MultiSeq window.