[Biojava-dev] [BioRuby] Interesting BLAST 2.2.25+ XML behaviour

[Chris Fields]

Haven't tried this using the latest BLAST+ myself, but it doesn't surprise me too much.  Also agree re: some kind of bug tracking with NCBI; I believe they have an internal one, but it would be nice to have a public interface to it.

chris

On May 3, 2011, at 4:24 AM, Peter Cock wrote:

> Hello all,
> 
> I've CC'd the BioPerl, BioRuby, BioJava and Biopython development mailing
> lists to make sure you're aware of this, but can we continue any discussion
> on the cross-project open-bio-l mailing list please?
> 
> I noticed that recent versions of BLAST are not using a single <iteration>
> block for each query, which was the historical behaviour and assumed
> by the Biopython BLAST XML parser. This may be a bug in BLAST.
> See link below for an example.
> 
> Has anyone else noticed this, and has it been reported to the NCBI yet?
> 
> Thanks,
> 
> Peter
> 
> (Not for the first time, I wish there was a public bug tracker for BLAST,
> or at least a private bug tracker so we could talk about issues with an
> NCBI assigned reference number.)
> 
> ---------- Forwarded message ----------
> From: Peter Cock <p.j.a.cock at googlemail.com>
> Date: Wed, Apr 20, 2011 at 6:08 PM
> Subject: Interesting BLAST 2.2.25+ XML behaviour
> To: Biopython-Dev Mailing List <biopython-dev at biopython.org>
> 
> 
> Hi all,
> 
> Have a look at this XML file from a FASTA vs FASTA search
> using blastp from  BLAST 2.2.25+ (current release), which
> is a test file I created for the BLAST+ wrappers in Galaxy:
> 
> https://bitbucket.org/galaxy/galaxy-central/src/8eaf07a46623/test-data/blastp_four_human_vs_rhodopsin.xml
> 
> I just put it though the Biopython BLAST XML parser, and
> was surprised not to get four records back (since as you
> might guess from the filename, there were four queries).
> 
> It appears this version of BLAST+ is incrementing the
> iteration counter for each match... or something like that.
> 
> Has anyone else noticed this? I wonder if it is accidental...
> 
> Peter
> 
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