BLAST
Overview
BLAST is the Basic Local Alignment Search Tool. It is a set of search
programs designed to explore all available sequence databases in either
protein or DNA. This software has been designed to achieve great speeds
while keeping a well-defined statistical interpretation.
Setup
No setup is needed to run BLAST.
Usage
BLAST provides a variety of commands including:
blastall
- performs protein-protein (blastp) searches,
- nucleotide-nucleotide (blastn) searches,
- nucleotide to protein database (blastx) searches,
- protein to translated nucleotide database (tblastn) searches,
- nucleotide to translated protein database (tblastx) searches,
- or position-specific interated (psiblastn) searches.
megablast
- performs nucleotide-nucleotide searches using an optimized
greedy algorithm that concatenates queries to save time
spent scanning the database.
blastpgp
- performs gapped blastp searches and can be used to perform
iterative searches in psi-blast and phi-blast mode.
bl2seq
- performs a comparison between two sequences using either
the blastn or blastp algorithm. Both sequences must be
proteins or both sequences must be nucleotides.
All standard NCBI BLAST databases (such as nr, nt, est) are available and
can be accessed as shown in the example section.
Examples
The following is an example PBS script to run a blastn job on LION-XE for
10 hours using both CPUs on a single compute node. The input query is
called queryn and is found in the directory /home/foo/blast. Output is
sent to the file queryn.out. The blastn search is run against the est
database.
#PBS -l nodes=1:ppn=2
#PBS -l walltime=10:00:00
#PBS -j oe
# change the current working directory to the directory where
# the input file queryn can be found
cd /home/foo/blast
# run the BLAST command using both processors on the compute node
# by including the '-a 2' option
blastall -p blastn -a 2 -d est -i queryn -o queryn.out
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Documentation
The official NCBI BLAST pages can be found at
http://www.ncbi.nlm.nih.gov/blast and contain a variety of
information on BLAST including a course and a
tutorial.
Please send questions or suggestions about this web page to beatnic@aset.psu.edu
ASET | ITS | Penn State
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