[BiO BB] PSI-BLAST query filter

[Iddo Friedberg]

OK, I still do not understand why blastpgp insists on filtering your
sequence... which version are you using?

Not that:

1) Using blastpgp You won't get a multiple alignment. You will get a
multiple pairwise alignment to the query sequence. Using ClustalW you will
get a true multiple alignment.

2) There is still an inherent problem when aligning low complexity
sequences.

3) If those two factors do not matter, then why not use blastall to build
your alignment? Why do oyu need the iterations blastpgp offers?

Curious,

./I



On Wed, 9 Mar 2005, Hongyu Zhang wrote:

> 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  -
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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
> >
> >
>