Hi, all, Since megablast has been replaced by blastn in newer NCBI BLAST tools, I am wondering if there is an update on megablast web interface and wrapper in Galaxy? Thanks, Luobin
On Fri, Mar 23, 2012 at 4:22 PM, Luobin Yang <yangluob@isu.edu> wrote:
Hi, all,
Since megablast has been replaced by blastn in newer NCBI BLAST tools, I am wondering if there is an update on megablast web interface and wrapper in Galaxy?
Yes, there are wrappers for the main tools from NCBI BLAST+ including blastn. They are included in the main Galaxy repository (but not available on the public Galaxy server due to the expected computational load). Peter
I've noticed these wrappers for BLAST+. I actually was talking about the megablast tool under NGS Mapping section... Thanks, Luobin On Fri, Mar 23, 2012 at 10:27 AM, Peter Cock <p.j.a.cock@googlemail.com>wrote:
On Fri, Mar 23, 2012 at 4:22 PM, Luobin Yang <yangluob@isu.edu> wrote:
Hi, all,
Since megablast has been replaced by blastn in newer NCBI BLAST tools, I am wondering if there is an update on megablast web interface and wrapper in Galaxy?
Yes, there are wrappers for the main tools from NCBI BLAST+ including blastn. They are included in the main Galaxy repository (but not available on the public Galaxy server due to the expected computational load).
Peter
On Fri, Mar 23, 2012 at 4:36 PM, Luobin Yang <yangluob@isu.edu> wrote:
I've noticed these wrappers for BLAST+. I actually was talking about the megablast tool under NGS Mapping section...
Thanks, Luobin
Oh - you mean update it to use BLAST+ instead of legacy BLAST internally? I asked about this too before writing the BLAST+ wrappers and one major concern was about breaking reproducibility - the newer BLAST doesn't give identical results. http://lists.bx.psu.edu/pipermail/galaxy-dev/2010-September/003342.html Also everything the megablast wrapper offers and more is in the blastn wrapper. Peter
Yeah, that's what I was wondering: to update megablast tool to use NCBI BLAST+ . I revised megablast wrapper a bit to use the legacy_blast.pl from NCBI BLAST+, but it seems the output format is not compatible with the tool (Fetch taxonomic representation) in metagenomic analyses anymore. So it looks like the only solution at the moment is to have both NCBI NCBI+ and an old version of BLAST. Thanks, Luobin On Fri, Mar 23, 2012 at 10:55 AM, Peter Cock <p.j.a.cock@googlemail.com>wrote:
On Fri, Mar 23, 2012 at 4:36 PM, Luobin Yang <yangluob@isu.edu> wrote:
I've noticed these wrappers for BLAST+. I actually was talking about the megablast tool under NGS Mapping section...
Thanks, Luobin
Oh - you mean update it to use BLAST+ instead of legacy BLAST internally? I asked about this too before writing the BLAST+ wrappers and one major concern was about breaking reproducibility - the newer BLAST doesn't give identical results. http://lists.bx.psu.edu/pipermail/galaxy-dev/2010-September/003342.html
Also everything the megablast wrapper offers and more is in the blastn wrapper.
Peter
On Fri, Mar 23, 2012 at 5:07 PM, Luobin Yang <yangluob@isu.edu> wrote:
Yeah, that's what I was wondering: to update megablast tool to use NCBI BLAST+ .
I revised megablast wrapper a bit to use the legacy_blast.pl from NCBI BLAST+, but it seems the output format is not compatible with the tool (Fetch taxonomic representation) in metagenomic analyses anymore.
So it looks like the only solution at the moment is to have both NCBI NCBI+ and an old version of BLAST.
Thanks, Luobin
I think that was what John Major was talking about earlier this month: http://lists.bx.psu.edu/pipermail/galaxy-dev/2012-March/008926.html Peter
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Peter Cock