Blast executables are aviable for Mac, PC(Win32), Linus, and Unix systems.
To run Blast locally, you need to (1) install blast executable and (2) format
a blast database. Instructions of installing blast on a Unix system can
be found at
http://genome.nhgri.nih.gov/blastall/blast_install/. The following
instructions assume you are installing on a PC(Win32).
1. Open the following FTP site use your web browser:
ftp://ftp.ncbi.nih.gov/blast/executables/.
2. Download blastz.exe, save it on local disk (e.g., c:\blast).
3. Installing Blast by double clicking on blastz.exe. Once done, you should see
a list of files in your c:\blast directory.
4. Next one needs to format the local database. GenBank databases can be downloaded
from NCBI databases (ftp://ftp.ncbi.nih.gov/blast/db/).
5. We here assume the local database file is in the FASTA format. Edit
a text file containing the following sequence:
>gi|532319|pir|TVFV2E|TVFV2E envelope protein
ELRLRYCAPAGFALLKCNDADYDGFKTNCSNVSVVHCTNLMNTTVTTGLLLNGSYSENRT
QIWQKHRTSNDSALILLNKHYNLTVTCKRPGNKTVLPVTIMAGLVFHSQKYNLRLRQAWC
HFPSNWKGAWKEVKEEIVNLPKERYRGTNDPKRIFFQRQWGDPETANLWFNCHGEFFYCK
MDWFLNYLNNLTVDADHNECKNTSGTKSGNKRAPGPCVQRTYVACHIRSVIIWLETISKK
TYAPPREGHLECTSTVTGMTVELNYIPKNRTNVTLSPQIESIWAAELDRYKLVEITPIGF
APTEVRRYTGGHERQKRVPFVXXXXXXXXXXXXXXXXXXXXXXVQSQHLLAGILQQQKNL
LAAVEAQQQMLKLTIWGVK
Save the sequence as c:\blast\testdb.txt. This will be our database.
Save again as c:\blast\query.txt, we'll use the same sequence as our query.
6. Open a MS-DOS window. Change directory to c:\blast (chdir c:\blast).
7. We'll name out database as "pacific". To format the database, using the following
command under MS-DOS:
formatdb -i testdb.txt -p T -n pacific
formatdb creats a number of new files.
8. Run Blast using the following command under MS-DOS:
blastall -p blastp -d pacific -i query.txt
9. For details on how to configure formatdb and BLAST, read the readme files.
Or type blastall under MS-DOS to show all options for BLAST.
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