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:
To compile, you just have to follow the instructions in the INSTALL files in the directories
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
in the database swiss, which is located in the directory given