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 <[email protected]>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 <[email protected]> wrote:

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Why can it be updated only once a year ?

Sent from my iPad

On Jan 10, 2013, at 3:57 PM, Folker Meyer <[email protected]> wrote:

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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 <[email protected]> wrote:

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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 <[email protected]> wrote:

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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 <[email protected]> wrote:

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... 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 < [email protected]> 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 <[email protected]> wrote:

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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:

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OK - that was some serious redundancy, but I think you catch my drift.

application specific syntactic sugar for specific apps.

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