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BLAST
Overview
The Basic Local Alignment Search Tool (BLAST) finds regions of local similarity between sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches. BLAST can be used to infer functional and evolutionary relationships between sequences as well as help identify members of gene families.
Two pre-compiled binary versions are available on the CSF:
- BLAST+ – a new suite of BLAST tools that utilizes the NCBI C++ Toolkit. The BLAST+ applications have a number of performance and feature improvements over the legacy BLAST applications. Versions 2.3.0 and 2.2.30 and 2.2.27 are available.
- BLAST (legacy) 2.2.26 – blastall, blastpgp, etc
For further information about the differences:
Restrictions on use
The software is public domain and available to all users. For further info load the BLAST+ modulefile and consult $BLASTP_HOME/LICENSE
Set up procedure
For BLAST+ load one of the following modulefiles:
module load apps/binapps/blast/blast+/2.4.0 module load apps/binapps/blast/blast+/2.3.0 module load apps/binapps/blast/blast+/2.2.30 module load apps/binapps/blast/blast+/2.2.27
and for BLAST (legacy):
module load apps/binapps/blast/legacy/2.2.26
If you have your own set of databases you will need a .ncbirc file in your home directory which tells BLAST where to find them. For example:
[BLAST]
BLASTDB=$HOME/genome_analysis/Blast/data
#
# The the correct path for where ever you store your own databases
Running the application
Please do not run BLAST on the login node. All work must be submitted to batch.
Serial batch job submission
Make sure you have the relevant modulefile loaded then create a batch submission script, for example:
#!/bin/bash #$ -S /bin/bash #$ -V #$ -cwd blastx -db efungi_pep_no_afua -query auto_351/contigs.fa -num_threads $NSLOTS -out 351un.out \ -evalue 1e-20 -max_target_seqs 1 -outfmt 6
Submit the job using:
qsub script
where script is the name of your jobscript file.
Parallel batch job submission
Make sure you have the relevant modulefile loaded then create a batch submission script, for example:
#!/bin/bash #$ -S /bin/bash #$ -V #$ -cwd #$ -pe smp.pe 4 blastx -db efungi_pep_no_afua -query auto_351/contigs.fa -num_threads $NSLOTS -out 351un.out \ -evalue 1e-20 -max_target_seqs 1 -outfmt 6
Submit the job using:
qsub script
where script is the name of your jobscript file.