Pre-formatted databases are available from a dedicated BLAST ftp site ftp://ftp.ncbi.nlm.nih.gov/blast/db/. Most BLAST databases on the NCBI site are updated on a daily basis.
A few commercial software packages are available for searching your own data. The advantage of using a commercial program is obvious when BLAST is integrated with the existing tools of these programs. Furthermore, they let you perform BLAST searches and retain annotations on the query sequence (see figure 13.21). It is also much easier to batch download a selection of hit sequences for further inspection.
Figure 13.21: Snippet of alignment view of BLAST results. Individual alignments are represented directly in a graphical view. The top sequence is the query sequence and is shown with a selection of annotations.