[BiO BB] PSI-BLAST query filter
forward at hongyu.org
Thu Mar 10 00:51:59 EST 2005
Thanks. Actually I did try the "-F F" option in blastpgp, but it
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
Quoting Iddo Friedberg <idoerg at burnham.org>:
> blastpgp "-F F" turns the filtering off, which is what you want
> which is the default, incidentally). I just checked blastpgp 2.2.5
> 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
> in PSI-BLAST? They'll bring you all sorts of non-specific stuff,
> will also be unrelated to the pattern you think you are searching
> 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
> >to create a PSI-BLAST alignment. The problem is that when running
> >PSI-BLAST, it will automatically filter out the low complexity
> >in the query sequence, which then will cause the query to have no
> >to the rest subject sequences. In BLASTP, I can just use the "-F
> >option to turn off the filter, but the PSI-BLAST (blastpgp)
> >seem to be affected by this option.
> >NCBI help desk provides little help unfortunately. Please let me
> >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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