On Tue, Sep 28, 2010 at 3:07 PM, Peter <peter(a)maubp.freeserve.co.uk> wrote:
On Tue, Sep 21, 2010 at 4:35 PM, Peter
>On Tue, Sep 21, 2010 at 4:14 PM, James Taylor <james(a)jamestaylor.org> wrote:
>> (I'd love to see a complete set of wrappers for NCBI blast+, which we could
>> include with our cloud images right away). Thanks!
> I'm working on it - we want to use it on our local server too.
I have a blastplus branch here, currently just minimal wrappers for blastn and
I've extended that to cover the five main BLAST flavours by adding blastx,
tblastn and tblastx. The order and descriptions should match that used on
the NCBI BLAST webserver.
Still to do, RPS-BLAST and PSI-BLAST, and of course most of the
Creating (small) databases from FASTA files seems potentially useful
(i.e. wrapping the BLAST+ tool makeblastdb which replaces formatdb)
but as these are made up of several files I need to know more about
how Galaxy works before tackling that.
Alternatively, the BLAST+ feature of FASTA file verses FASTA file
could be handy (using -subject instead of -db). I think I can see how
to handle this... but it would complicate supporting other parameters.