[BiO BB] PSI-BLAST query filter

[Hongyu Zhang]

Dear all,

I have a group of low complexity sequences here, based on them I want
to create a PSI-BLAST alignment. The problem is that when running
PSI-BLAST, it will automatically filter out the low complexity region
in the query sequence, which then will cause the query to have no hit
to the rest subject sequences. In BLASTP, I can just use the "-F f"
option to turn off the filter, but the PSI-BLAST (blastpgp) doesn't
seem to be affected by this option.

NCBI help desk provides little help unfortunately. Please let me know
if any of you have solutions. Thanks in advance.


--
Hongyu Zhang
Computational biologist
Ceres Inc.