To execute a BLAST program, we first launch a DOS command prompt, which is generally kept under: Start, Program, Accessories, Command Prompt. A launching session (A) and the resulting command prompt (B) are shown in Figure 2.1.4.1.
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Figure 2.1.4.1 Opening of a DOS command prompt (white) under
Window XP.
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In this prompt, we change the working directory to 'E:\blast-2.2.15' by typing 'E:' and enter key stroke, followed by "cd blast-2.2.15" and enter key stroke. We also create the db directory using "mkdir db" and display the directory content using 'dir'.
To make windows aware of the location of blast programs, we need to add the path 'E:\blast-2.2.15\bin\' to the PATH environment variable. To do so, click on 'Start, Settings, Control Panel', then the System Icon. In the new prompt, click on 'Advanced' tab, 'Environment Variables' button, and click on 'New' in the User section to add a new variable called PATH with 'E:\blast-2.2.15\bin\' as its value. If you are the administrator, you can modify the PATH environmental varial in the system section by terminating the existing PATH string with a semicolon (;) and appending 'E:\blast2211\bin\' (without the quotes) after it.
This change will enable us to call BLAST programs, using their name followed by the appropriate option value pairs as input, from any directory in the computer. For example, we can use the following command line to call blastall, use its blastn subprogram, search against refseq_rna database with fasta_query.txt as query, and save the result in output.txt:
blastall -p blastn -d refseq_rna -i fasta_query.txt -o ouput.txt
The refseq_rna is an NCBI database from the db subdirectory ftp://ftp.ncbi.nih.gov/blast/db. It is in preformatted form and can be used immediately after WinZip extraction. For more information, see: ftp://ftp.ncbi.nih.gov/blast/documents/blastdb.html.
To further customize the search, we can manipulate the relevant search parameters by referring to the parameter list in Section 3 below.