The blast programs are in the public domain, and can be obtained by ftp from ncbi.nlm.nih.gov/blast. Currently there are two versions installed at our site:
~/blast1.3 and
~/blast1.4.
To compile, you just have to follow the instructions in the INSTALL files in the directories ~/blast1.3/blast and
~/blast1.4/blastapp respectively.
The blast programs use the following environment variables, which when not defined, the values are taken from the equally named constants defined in blastapp.h.
To run a blast program, you have to specify at least the database to
use and the query sequence to search for. For example:% blastp swiss ~/queries/protpart1.seq
searches the query contained in the file ~/queries/protpart1.seq
in the database swiss, which is located in the directory given
by BLASTDB.