Question about blastp result

Question

[huiyus97]

Hi,

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!

[lieven.sterck]

hard to tell without having more detailed info.

are you running the same parameter settings? same blast version? same database version? ...

One thing already is that using -max_target_seqs is quite tricky (do some searching on this forum as well as internet for this and you will quickly notice)

Also, why do you assume you're getting too much hits, perhaps the company is reporting way too few hits?

[GenoMax]

Did you use an identical copy of the database, blast program and parameters? This may not be a problem at all. If one or more of the things mentioned in first sentence differ then your result will also be different.