We have performed BLAST searches online at NCBI, and through VectorNTI. Because BLAST searches are such an integral part of bioinformatics, you can run them in many ways. SeqWeb also allows you to run BLAST searches.

To run a BLAST search:

1. Click on the SeqWeb icon to return to the selection page
2. Click on either of these links to access the BLAST suite:

or

3. Choose the sequence that you want, and the database that you want to BLAST it against. You can then click the run icon to start the BLAST.
4. This window will change and display a clock something like this   Click on the Cancel button to stop the program mid-run if you want to.

5. The results will open in a new window like this:



 

6. You now have several choices
1. You can click on alignment to view the alignments for each of the sequences
2. You can click on the accession number (eg GB_BA:AF043239) to view the sequence
3. You can check one of the check boxes: and then click to add the selected sequence to your list of sequences
4. You can save the results in HTML or plain text format

SeqWeb has two varieties of BLAST, regular BLAST and NETBLAST. The regular BLAST runs the searches against the local version of the databases, but the NETBLAST runs the searches at NCBI. Although the local BLAST maybe quicker, the database is usually out-of-date.

For example, at the time of writing this, the two databases used by BLAST and NETBLAST are shown in the table below:

In the next section we will look at some features of SeqWeb that cannot be done in vectorNTI.