OK. So what happened in this conversation? Are we going to offer a
sequence search capability? Who's involved in the campaign? Who's leading
it? Which sequence databases will be part of it? How will it integrate
with the other (keyword?) search service / GUI?
Thanks,
- Dylan
On Thu, Jan 10, 2013 at 1:04 PM, Folker Meyer <folker.meyer(a)gmail.com>wrote:
> we have >20 TBp of data.....
>
> experience shows this is kind of hard to re-analyze..... and takes some
> time
>
>
> On Jan 10, 2013, at 3:03 PM, Rick stevens <stevens(a)anl.gov> wrote:
>
> > Why can it be updated only once a year ?
> >
> > Sent from my iPad
> >
> > On Jan 10, 2013, at 3:57 PM, Folker Meyer <folker(a)anl.gov> wrote:
> >
> >> I see your point, but the underlying requirements for communities are
> such that we can only update once a year. AND we need to be able to support
> other namespaces....
> >>
> >> can we subject the other areas to the only one update per year
> requirement?
> >>
> >> Best,
> >> Folker
> >> On Jan 10, 2013, at 2:37 PM, Rick stevens <stevens(a)anl.gov> wrote:
> >>
> >>> We need a coherent NR for KBase.
> >>>
> >>> Not one for microbes and one for communities.
> >>>
> >>>
> >>> Sent from my iPad
> >>>
> >>> On Jan 10, 2013, at 3:24 PM, Folker Meyer <folker(a)anl.gov> wrote:
> >>>
> >>>> Dylan,
> >>>>
> >>>> good idea. actually this is a great service for people wanting to
> search metagenomes, I encourage you to build it.
> >>>>
> >>>> It should do exactly what you suggest:
> >>>>
> >>>> - any sequence input is searched against the m5nr
> >>>> - retrieve md5s for the m5nr entries
> >>>> - retrieve list of metagenome_IDs that this md5 is present in
> >>>> - find any sequences matching the md5s in your metagenome(s) of
> choice with very loose cut-offs
> >>>> - re-run a BLAST(?) or some other search on the sequence set and
> return things that hit for real with good (strict) cut-offs.
> >>>>
> >>>> We will have to implement an Md5->metagenome_ID function (we can do
> that if you decide to go for this)
> >>>>
> >>>> I think this would be an excellent service to offer, it might be
> resource constraining, but this is definitely something that a lot of users
> have asked for in the past.
> >>>>
> >>>> Best,
> >>>> Folker
> >>>>
> >>>>
> >>>> On Jan 10, 2013, at 12:07 PM, Dylan Chivian <dcchivian(a)lbl.gov>
> wrote:
> >>>>
> >>>>> ... and what about searching metagenomic sequence? (i'd wink, but
> it's not funny)
> >>>>>
> >>>>> since these guys use the m5nr, we could expand any hit from a query
> sequence to an m5nr sequence into the mg reads that are close to the m5nr
> exemplar. just a thought. any other ideas?
> >>>>>
> >>>>> thanks,
> >>>>> - dylan
> >>>>>
> >>>>>
> >>>>> On Wed, Jan 9, 2013 at 8:55 PM, Christopher Henry <
> chrisshenry(a)gmail.com> wrote:
> >>>>> Well, it's a fair question.
> >>>>>
> >>>>> First, we are going to have users, like me, who specifically want to
> run specific BLAST queries for specific reasons. For that, I think we need
> a BLAST server. I for one want a blast query to look for specific sequence
> without having to worry about whether or not the gene callers missed this
> gene. In particular, this is something we are speculating is a universal
> gene, and so for the genomes where we don't find it already, we want to do
> a REALLY thorough search. Does this make sense? So I was thinking TBlastN
> is what I want… even if it is painfully slow and inefficient… it's to meet
> this very specific need… and I won't be using it to process a ton of
> sequence. Just query 10 or so diverse versions for this protein.
> >>>>>
> >>>>> I posit… given the increasing drive towards protein speculation and
> resolving more challenging problems in annotation, this is going to be a
> common use scenario.
> >>>>>
> >>>>> Second, it's completely fair to say we need a service that says "I
> have a sequence that I want to find what KB knows about". It's a separate
> use scenario in my mind. It's almost a search query, and the sim service is
> darn close to being able to handle this particular use scenario.
> >>>>>
> >>>>> On Jan 9, 2013, at 2:43 PM, Robert Olson <olson(a)mcs.anl.gov> wrote:
> >>>>>
> >>>>>> Do we really mean "BLAST" in particular, or is the problem really
> "I have sequence that I want to find what KB knows about" ?
> >>>>>>
> >>>>>> On Jan 9, 2013, at 2:41 PM, Shreyas Cholia wrote:
> >>>>>>
> >>>>>>> OK - that was some serious redundancy, but I think you catch my
> drift.
> >>>>>>>
> >>>>>>> application specific syntactic sugar for specific apps.
> >>>>>>>
> >>>>>>>
> >>>>>>> _______________________________________________
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> >>>>>>> https://lists.kbase.us/mailman/listinfo/kbase-devel
> >>>>>>
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> >>>>>> https://lists.kbase.us/mailman/listinfo/kbase-devel
> >>>>>
> >>>>> _______________________________________________
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> >>>>
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> >>
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