[Bioperl-l] If you use RemoteBlast

Barry Moore bmoore at genetics.utah.edu
Mon Aug 29 18:13:56 EDT 2005


I stepped through the code in
Bio::Tools::Run::RemoteBlast::submit_blast, and bioperl is using the
default new formatter, and for the dozen or so nucleotide sequences that
I ran no problems parsing.


-----Original Message-----
From: bioperl-l-bounces at portal.open-bio.org
[mailto:bioperl-l-bounces at portal.open-bio.org] On Behalf Of Jason
Sent: Monday, August 29, 2005 10:18 AM
To: Bioperl List
Subject: [Bioperl-l] If you use RemoteBlast

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.


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  
> 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

> 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? 
> 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? 
> 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

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