[BiO BB] PSI-BLAST query filter

Iddo Friedberg idoerg at burnham.org
Wed Mar 9 21:15:13 EST 2005

blastpgp "-F F" turns the filtering off, which is what you want (and 
which is the default, incidentally). I just checked blastpgp 2.2.5 and 
it does not filter low complexity sequences. In blastall, the default is 
"-F T"; this is done to confuse us and keep us on our toes.

The broader picture: why would you want to use low complexity sequences 
in PSI-BLAST? They'll bring you all sorts of non-specific stuff, which 
will also be unrelated to the pattern you think you are searching for. 
There are programs to search for low complexity regions. 0j.py comes to 
mind, but there are others.



Hongyu Zhang wrote:

>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.
>Bioinformatics.Org general forum  -  BiO_Bulletin_Board at bioinformatics.org

Iddo Friedberg, Ph.D.
The Burnham Institute
10901 N. Torrey Pines Rd.
La Jolla, CA 92037 USA
Tel: +1 (858) 646 3100 x3516
The First Automated Protein Function Prediction SIG
Detroit, MI June 24, 2005

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