Return not aligned with BLAST

[ffalfred]

Hello,

I am new to Seqanswers, though not to Bioinformatics.

I have a doubt with BLAST. Is there a simple way to get all the sequences, after blasting one database to another database, that have not been aligned (under a e-value threshold)?

[Brian Bushnell]

If you can grab the headers of the sequences that were aligned, you can use BBMap's filterbyname.sh or a similar tool to remove them from the source fasta.