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Star Republic: Guide for Biologists

Local Blast

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.