Is it correct to use subject instead of db in blast command?

Question

[logbio]

blastp -query homo.faa -db cow.faa -out homo_blast.csv -outfmt 6 -evalue 0.00001 -max_target_seqs 1 -num_threads 32

I got the below error while performing protein blast with the code mentioned above

BLAST Database error: No alias or index file found for protein database [cow.faa] in search path

When I revised the code by specifying the path, the problem was not resolved. When I typed subject instead of db, the problem was solved, but I'm not sure if it's correct.

Answer 1

[Mensur Dlakic]

When you use a -db switch, it is expected that your database will be indexed. This is done using a makeblastdb command, and will create several files that will end in .p?? where ?? stands for two other letters. When searching against a large database, to gain speed you would want to index it and use a -db switch. You most likely have not done this step.

When using a -subject switch, the database need not be indexed. The result will be the same as when using the -db switch, but the search will be slower and this is not recommended for larger databases. It is typically used for comparing two sequences, or when the target database is relatively small.

[logbio]

Thank you!