BLAST+
Overview
BLAST+ is a command-line version of the Basic Local Alignment Search Tool (BLAST) provided by the National Library of Medicine to compare biological sequences to databases and find their similarities.
Availability
| Cluster | Module/Version |
|---|---|
| BOSE | blast/2.15.0 |
| BGSC | Not Available |
Note: You can simply use module load blast to activate the most recently installed version of this software.
Arguments / Options
This is a list of arguments for the BLAST+ commands that we wanted to highlight. Use command -help or view the official user manual for a full list.
| Option | Description |
|---|---|
| -help | List of available arguments and their descriptions |
| -db | Which sequence database to compare against? Defaults to search our local database repository |
| -query | Input file name |
| -out | Output file name |
Local Databases
For our users' benefit, we have made available a local copy of requested BLAST databases. These are available under the $BLASTDB environment variable, which BLAST+ automatically uses by default.
These databases are automatically updated every weekend.
Currently Installed:
- nr
- nt
- refseq_protein
- taxdb
If you have a database you'd like us to set up, let us know which one you'd like by looking at section three here: https://ftp.ncbi.nlm.nih.gov/blast/documents/blastdb.html.
Sample Slurm Script
#!/bin/bash
# -- SLURM SETTINGS -- #
# [..] other settings here [..]
# The following settings are for the overall request to Slurm
#SBATCH --ntasks-per-node=32 # How many CPU cores do you want to request
#SBATCH --nodes=1 # How many nodes do you want to request
# -- SCRIPT COMMANDS -- #
# Load the needed modules
module load blast # Load BLAST+
blastp -db nt -query myfile.fa
Real Example
Has your research group used BLAST+ in a project? Contact the HPC Team and we'd be glad to feature your work.
Citation
Please include the following citation in your papers to support continued development of BLAST+.
Camacho, C., Coulouris, G., Avagyan, V., Ma, N., Papadopoulos, J., Bealer, K., & Madden, T.L., 2009. BLAST+: architecture and applications. BMC Bioinformatics, 10, 421.
If you are using a database that you did not generate, such as one from GenBank, make sure to properly cite those as well.
See this page from the National Library of Medicine for more information on citing NCBI services and databases. There is also a link to a page containing various examples of citations.