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@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@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@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@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@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@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@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@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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