[Bioperl-l] If you use RemoteBlast

[Paulo Almeida]

I think it is indeed the new formatter that is being requested by 
Tools::RemoteBlast, since it is the default and Tools::RemoteBlast doesn't 
seem to change it (I'm using BioPerl 1.4).

There is this checkbox in Blast.cgi that controls this:

<input checked name="NEW_FORMATTER" type="checkbox">

I don't know if there are more complex ways in which the new formatter may 
break the parser, but I've been using Tools::RemoteBlast and didn't notice 
anything weird (my code is pretty much the same as the Synopsis).

-- Paulo

On Monday 29 August 2005 17:18, Jason Stajich wrote:
> So those of you who use the Tools::RemoteBlast module, please read
> the following email.    We need some people to test out how much the
> parser breaks with the "new" formatter. Tests seem to pass right now,
> but I don't know if that is because the 'old' format is being
> requested still.  Could someone please take a little time to see
> what's going on and report back.
>
> Thanks,
> -jason
>
> Begin forwarded message:
> > From: "Mcginnis, Scott (NIH/NLM/NCBI)" <mcginnis at ncbi.nlm.nih.gov>
> > Date: August 29, 2005 12:06:52 PM EDT
> > To: "'jason at bioperl.org'" <jason at bioperl.org>
> > Subject: New BLAST Formatter.
> >
> >
> > Hello.
> >
> > The new BLAST formatter has been a default for a months now. But
> > we'd like
> > to shut off the old one.
> >
> > Will this pose a problem?
> >
> > Thanks,
> >
> > Sincerely,
> > Scott D. McGinnis, M.S.
> > National Center for Biotechnology Information
> > <http://www.ncbi.nlm.nih.gov>
> >
> >
> > Blast-announce: New BLAST formatter at the NCBI
> >
> > A new version of the BLAST formatter has been the default on the
> > NCBI BLAST
> > web pages for the past XX months.  On September 6, 2005 we will
> > remove the
> > checkbox allowing users to select the old formatter and support for
> > the old
> > formatter will be discontinued.
> >
> > This formatter has been rewritten from scratch using the NCBI C++
> > toolkit
> > and includes many new features (see list below) as well as the
> > ability to
> > fetch parts of genomic sequences when needed, making it much faster
> > than the
> > old formatter for many queries.
> >
> > Please send questions or comments to blast-help at ncbi.nlm.nih.gov
> >
> >
> > New features:
> > --------------
> >
> > 1.) The new formatter will present the masked residues or bases as
> > lower-case letters.  Additionally the masked letters can be shown
> > in color.
> > To use this feature change the "Masking Character" to "Lower case"
> > on the
> > formatting page and select a "Masking Color".
> > Example:
> >
> > http://www.ncbi.nlm.nih.gov/BLAST/Blast.cgi?
> > CMD=Get&RID=1098448824-15725-370
> > 06897750.BLASTQ4&NEW_FORMATTER=on&MASK_CHAR=2&MASK_COLOR=2&DESCRIPTION
> > S=0
> >
> >
> > 2.) The "pairwise with identities" option allows easy
> > identification of a
> > few mismatches among highly similar sequences. In this (pair-wise)
> > view
> > mismatches, as well as "Sbjct" (on the line containing the
> > mismatch) are
> > shown in red.
> > To use this feature change the "Alignment view" to "Pairwise with
> > identities" on the formatting page.
> > Example:
> >
> > http://www.ncbi.nlm.nih.gov/blast/Blast.cgi?
> > CMD=Get&NCBI_GI=yes&SHOW_OVERVIE
> > W=on&ALIGNMENT_VIEW=PairwiseWithIdentities&NEW_FORMATTER=on&RID=111089
> > 2196-1
> > 6209-7903412953.BLASTQ4#28302128
> >
> >
> > 3.) For database sequences longer than 200,000 bases each alignment
> > has a
> > header entitled "Features in this part of the subject sequence"
> > listing CDS features on the database sequence within the alignment
> > range or
> > at the 5' or 3' end if not features are within the range itself.
> > This gives a quick description of what you are looking at as many long
> > sequences have a standard defline such as "chromosome 16".
> > Example:
> >
> > http://www.ncbi.nlm.nih.gov/blast/Blast.cgi?
> > CMD=Get&NCBI_GI=yes&SHOW_OVERVIE
> > W=on&NEW_FORMATTER=on&RID=1098455471-18771-167762343145.BLASTQ4#514656
> > 96
> >
> >
> > Rewrites/bug fixes:
> > -------------------
> >
> > 1.) The graphic overview has been rewritten; it now uses an HTML
> > implementation.
> >
> > 2.) Query-anchored views now work with blastx/tblastn/tblastx, they
> > didn't
> > before.
> >
> > 3.) phi-BLAST patterns are now also shown in the query-anchored view.
>
> --
> Jason Stajich
> Duke University
> http://www.duke.edu/~jes12
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at portal.open-bio.org
> http://portal.open-bio.org/mailman/listinfo/bioperl-l

-- 
Paulo Almeida
Tel: +351 21 4464635, Fax: +351 21 4407970
Instituto Gulbenkian de Ciência
Rua da Quinta Grande, 6
P-2780-156 Oeiras
Portugal
http://www.igc.gulbenkian.pt