On Thu, Mar 31, 2011 at 6:28 PM, Peter Cock <p.j.a.c...@googlemail.com> wrote:
> Hi all,
>
> The NCBI have just released BLAST 2.2.25+ which includes some
> interesting new stuff of interest to the tabular output, i.e.
>
> "Added support for query and subject length to tabular output"
>
> I would therefore like to update my BLAST+ wrappers in Galaxy to add
> these two columns to the 'extended tabular' output option. They are going
> to be very helpful as you can now calculate things like the percentage
> identity (or similarity) compared to the query or sequence.
>
> If there are no objections I propose to add these as columns 23 and 24
> (i.e. at the end), so minimise disruption to anyone already using the
> tabular output. I would hope to have a branch ready for merging next
> week...

One reason why I want to move to BLAST 2.2.25+ on our local
machine is they fixed the subject IDs in tabular output, so that I
can now use BLAST to compare two FASTA files against each
other for a reciprocal best hits (RBH) search. I've just pushed the
first draft of this to my bit-bucket,

https://bitbucket.org/peterjc/galaxy-central/changeset/198bf927ca30

The idea behind this tool is to allow RBH to be done using any
suitable tabular input - including but not limited to the BLAST
tabular output (which can also be mimicked by other tools such
as Bill Pearson's FASTA).

I'm hoping this will be accepted into Galaxy later on (it is not
ready yet), but I will need some help with this issue first:

http://lists.bx.psu.edu/pipermail/galaxy-dev/2011-March/004799.html
https://bitbucket.org/galaxy/galaxy-central/issue/507/

Thanks,

Peter
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