Can BLAST+ download aligned sequences after using BLASTp like BLAST web site?

Question

[ZHIRUI]

I have a huge data that needs to be aligned, and I want to use blast+ to complete it. I want to ask whether blastp in BLAST+ can output similar to the download aligned sequences on the BLAST_Website.

Thank you.

Answer 1

[5heikki]

You can e.g. use custom tabular output format and include sseq means Aligned part of subject sequence. Then it's a matter of of a simple awk command to create a fasta file from the blast output file. See blastn -help