I need to blast several proteomes against several databases, and I found that I got way too many blastp result compared to the blastp result we got from a company using the same proteome and against the same database. For example, I blasted a proteome against the PHI database using this code:
$blastp -in input.fasta -evalue 1e-5 -outfmt 6 -out outfile -db database.fasta -max_target_seqs 1
As a result, I got 4000 proteins with a e-value=1e-5, however, the company got 1400 proteins with the same e-value.
Could someone please tell me what causes this problem?
Thanks in advance!