The Basic Local Alignment Search Tool (BLAST) is the most widely used sequence similarity tool. BLAST can compare protein queries to protein databases, nucleotide queries to nucleotide databases, as well as translate nucleotide queries or databases in all six frames and compare to protein databases or queries.  BLAST+ is 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.

To run this software interactively in a Linux environment run the commands:

module load ncbi_blast+

Once you have set up your environment, you can use any of the BLAST programs directly, e.g.

blastn -db nt -query nt.fsa -out results.out

will run a search of nt.fsa against the nt database.

Local databases for BLAST searches are available in


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