How-to BLAST

This page will tell you how to run NCBI's Basic Local Alignment Search Tool (BLAST) using a command line prompt. NCBI also has a web-based BLAST that you can run here.

1. Download the BLAST+ tool kit for your operating system.

2. Download the necessary database.

-For the Sawyer et al. (2011) paper, we wanted the non-redundant (nr) database of all known protein sequences—nr.00.tar.gz, etc. For the directory of databases, see this link.            

3. Obtain query file in FastA format.


4. Choose your parameters.

The BLAST command

You code a BLAST command by giving parameters designated by a single letter with a dash in front. Generally, lowercase letters refer to the input and uppercase letters refer to the output. Our BLAST call:

-designates where the computer can find the program and which version of the program to use (-p, blastp for protein BLAST)
-the name of the input (-i)
-the database to BLAST against (-d, name includes where to find that database)
-type of statistics to use (-C, computational)
-format of output (-m)
-name of output (-o)

We add on other information that is specific to our computer, such as how many processors to use and courtesy settings if other people need to run a program.

An example call:

blastall (call blastall program) –p (type of input, -p means protein) blastp (sub-program, run protein blast) –b 100 (maximum 100 hits, default is 250) –i input.fa (input file) –d nr (databasefile) –m 8 (output format option 8) –o output.txt (output file) –e 0.01 (quality control level e=0.01)

Our call for the Sawyer et al. (2011) paper:

/localapps/blast-2.2.18/bin/blastall -p blastp -i input.fa -d data/gb/nr -C 2 -m 8 -o output.blast

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Copyright 2011 Last Modified 4/2011