The BLAST package can be downloaded free of charge from the following location http://www.ncbi.nlm.nih.gov/BLAST/download.shtml
Pre-formatted databases are available from a dedicated BLAST ftp site ftp://ftp.ncbi.nlm.nih.gov/blast/db/. Moreover, it is possible to download programs/scripts from the same site enabling automatic download of changed BLAST databases. Thus it is possible to schedule a nightly update of changed databases and have the updated BLAST database stored locally or on a shared network drive at all times. Most BLAST databases on the NCBI site are updated on a daily basis to include all recent sequence submissions to GenBank.
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 11.25). It is also much easier to batch download a selection of hit sequences for further inspection.
Figure 11.25: Snippet of alignment view of BLAST results from CLC Main Workbench. Individual alignments are represented directly in a graphical view. The top sequence is the query sequence and is shown with a selection of annotations.