If the path to blast-2.2.15/bin directory is not included in the PATH environment variable, we will need to call blast programs by prefix the path before the program name. For example, under blast-2.2.15 directory, we need to call blastall this way:
./bin/blastall -
where "./bin" portion of the command instructs shell to look in the bin subdirectory under the working directory. This command line example will display all the command line parameters for blastall on the screen. Actual search will require additional option/value inputs. The path to matrix and database will not be needed once the .ncbirc is configured properly. We need to make sure that downloaded databases are placed in the db subdirectory.