[BiO BB] PSI-BLAST query filter

[Hongyu Zhang]

Thanks. Actually I did try the "-F F" option in blastpgp, but it
doesn't work.

I am not using PSI-BLAST to do any search. I am just trying to
generate an alignment give a group of low complexity sequences. I
could use ClustalW, but my downstream program requires PSI-BLAST
alignment format.

--
Hongyu Zhang
Computational biologist
Ceres Inc.



Quoting Iddo Friedberg <idoerg at burnham.org>:

> 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.
>
> best,
>
> Iddo
>
> 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
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> >
> >
> >
> >
>
>
> --
> Iddo Friedberg, Ph.D.
> The Burnham Institute
> 10901 N. Torrey Pines Rd.
> La Jolla, CA 92037 USA
> Tel: +1 (858) 646 3100 x3516
> http://ffas.ljcrf.edu/~iddo
> ==========================
> The First Automated Protein Function Prediction SIG
> Detroit, MI June 24, 2005
> http://ffas.burnham.org/AFP
>
>