I have a new sequence and I want to add it to a pre-constructed BLAST database containing other sequences. The makeblastdb help does not give any hint on this regard.
You can use
blastdbcmd to extract FASTA sequences from the BLAST database. Then you can append your extra sequence to the newly created FASTA file, and remake the BLAST DB using
makeblastdb. Assuming you have a protein BLAST database in the current working directory, and a sequence you want to add to it in
$ blastdbcmd -db proteindb -dbtype prot -out db.fa -entry all $ cat new.fa >> db.fa $ makeblastdb -in db.fa -out newproteindb -dbtype prot
nucl if you have a nucleotide database)