[BiO BB] PSI-BLAST query filter

Hongyu Zhang forward at hongyu.org
Wed Mar 9 20:39:54 EST 2005

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.

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