Step 1: FTP the Web Server Package
are located in the current_release directory. Releases are
available for Linux/Intel OSF/DEC-Alpha SGI and Solaris/Sun
Unpack the distribution into any local document directory under the HTTPD server directory that has permission to run CGI programs with a *.cgi file extension. The BLAST Web server package is a Gzipped tarred archive. Gunzip the archive using a command such as:
untar the archive using:
the use of the p or preserve TAR option. This option preserves the
file protections as they existed when the files were archived. This is
essential to allow the proper access to all files by the server software.
Uncompressing the archive will create a directory called blast which
contains all the files needed to implement the WWW BLAST server.
Format the local databases that you wish the server to use. This is accomplished in the usual manner using the program formatdb included in the server package. The database files should be placed in the db directory which is created when you untar the archive. To format a database for BLAST use:
formatdb -i infile -o T
that databases to be used with PSI- or PHI-BLAST should always be created
using the -o T flag.
server package comes with two BLAST databases called test_aa_dba
sample protein database and test_na_dba sample
nucleotide database. These databases are configured to be used immediately.
Perform a test search on these database using the blast.html
add your own databases to the list used by the server you must edit
two configuration files called blast.rc and psiblast.rc.
These files specify the combinations of database names and BLAST program
that are considered valid. Below is an excerpt from the file blast.rc
as it appears out of the box.
The line blastn test_na_db for example specifies that the database named test_na_db is valid when used with the blastn program. To add another nucleotide database to the list searchable by blastn simply add its name to this line so that it now reads:
blastn test_na_db new_database
new database name must also be added to the html search forms in order
to appear in the pull-down database menu boxes so the blast.html
file also needs to be edited. The relevant lines for blast.html are:
Run your first flawless test of the BLAST server!