ncbi-blast bsml and wu-blast bsml

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ncbi-blast bsml and wu-blast bsml

Aaron Buechlein
Hello,
We are working towards using ncbi-blast in place of wu-blast going
forward.  In working towards converting our pipelines to use ncbi-blast,
I noticed that the bsml is different for ncbi-blast compared to the bsml
for wu-blast.  For instance, in the Prokaryotic Annotation Pipeline,
pipeline_summary fails if you substitute ncbi-blastp for the COG search
because the bsml file produced does not contain a p-value entry.  Is one
of the bsml output styles preferred over the other?
Thanks,

Aaron Buechlein

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Re: ncbi-blast bsml and wu-blast bsml

Joshua Orvis
Aaron -

Given that WU-BLAST is no longer available, and I don't know anyone working with AB-BLAST yet within Ergatis, I'd say we make sure that our NCBI-BLAST output is as robust as possible and focus on that.  In the ncbi-blast components the output is first transformed into btab, a tab-delimited format, and then into BSML.  This btab has columns for both E-value (20) and P-value (21), so both could be accommodated if present.

I see that the NCBI-blast BSML places it in the 'runprob' attribute of the Seq-pair-run element instead of its own Attribute element.  It should be less disruptive to add the missing element rather than remove the 'runprob' attribute.

Thoughts from anyone whose components or pipelines rely on the BSML output of the NCBI-family of components?

Joshua



On Thu, May 20, 2010 at 1:09 PM, Aaron Buechlein <[hidden email]> wrote:
Hello,
We are working towards using ncbi-blast in place of wu-blast going
forward.  In working towards converting our pipelines to use ncbi-blast,
I noticed that the bsml is different for ncbi-blast compared to the bsml
for wu-blast.  For instance, in the Prokaryotic Annotation Pipeline,
pipeline_summary fails if you substitute ncbi-blastp for the COG search
because the bsml file produced does not contain a p-value entry.  Is one
of the bsml output styles preferred over the other?
Thanks,

Aaron Buechlein

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