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Update on Megablast?

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Update on Megablast?

Luobin Yang
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Since megablast has been replaced by blastn in newer NCBI BLAST tools, I am wondering if there is an update on megablast web interface and wrapper in Galaxy?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

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Re: Update on Megablast?

Peter Cock
On Fri, Mar 23, 2012 at 4:22 PM, Luobin Yang <[hidden email]> 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 Since megablast has been replaced by blastn in newer NCBI BLAST tools, I am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
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Re: Update on Megablast?

Luobin Yang
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 <[hidden email]> wrote:
On Fri, Mar 23, 2012 at 4:22 PM, Luobin Yang <[hidden email]> 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 Since megablast has been replaced by blastn in newer NCBI BLAST tools, I am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


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Re: Update on Megablast?

Peter Cock
On Fri, Mar 23, 2012 at 4:36 PM, Luobin Yang <[hidden email]> 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
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Re: Update on Megablast?

Luobin Yang
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 <[hidden email]> wrote:
On Fri, Mar 23, 2012 at 4:36 PM, Luobin Yang <[hidden email]> 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


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Re: Update on Megablast?

Peter Cock
On Fri, Mar 23, 2012 at 5:07 PM, Luobin Yang <[hidden email]> 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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