blastn a list of sequences against themselves

[AVesterbacka]

Hello,

I have a small problem with blast. I'm trying to blast a set of sequences using the same set of sequences as the database, but there are a few sequences that get 0 hits. How can this be? Shouldn't blastn atleast find the same sequence (which is the case in most of my sequences)? The minimum sequence length that I have in the list is ~200nt, and even most of the these do find themselves as a hit. The sequences that don't find any hits seem to have quite a lot of repeat (AGAGAG, GTGTGT, TTTTTT, etc.), so could this be the "problem"?

[swbarnes2]

You can turn of complexity filtering in blast. Try doing that, and those sequences should blast to themselves.

[westerman]

. The sequences that don't find any hits seem to have quite a lot of repeat (AGAGAG, GTGTGT, TTTTTT, etc.), so could this be the "problem"?

Yes. Look at the '-dust' option in regards to default low-complexity filtering.