[BiO BB] PSI-BLAST query filter

[Hongyu Zhang]

Iddo,

What I meant is using "-m 1" option in blastpgp to create an alignment
view of multiple sequences. The version of my blast program is 2.2.8
running on Linux.

I prefer blastpgp because it allows me the flexibility to do multiple
iterations to increase the alignment accuracy. You are right that, in
the end, I might have to use blastall to generate alignment if
blastpgp keeps giving me trouble.

Thanks!

--
Hongyu Zhang
Computational biologist
Ceres Inc.



Quoting Iddo Friedberg <idoerg at burnham.org>:

>
> 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  -
> > > BiO_Bulletin_Board at bioinformatics.org
> > > >https://bioinformatics.org/mailman/listinfo/bio_bulletin_board
> > > >
> > > >
> > > >
> > > >
> > >
> > >
> > > --
> > > 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
> > >
> > >
> >
>
>