On May 16, 2013, at 3:43 PM, Rick Stevens <[email protected]> wrote:

in the WGS Metagenome contig example in most cases you don't have 16s .so you would need to do some kind of best guess from the protein sequences and probably not just one protein but some kind of voting or perhaps a classifier specially designed for this.

we have a naive scheme for inferring taxonomic origin. Actually 3 schemes. Described in the FAQ. all of them rely on using similarities. The LCA probably gives you the most reliable answers, but it is classifying to varying levels. A good way forward would be a filter that uses the ~50 ribosomal proteins instead/in addition to the 16s. That could be a good thing to implement.

It clearly could be and would be computed when the MG is processed .. but then you would need to work out how to decide what to call something if the match is not great or you have hits with no clear consensus (which is what we see sometimes).

Yes. deciding which thresholds to use is the hard part. MG-RAST defers that decision to the user. The user sets parameters at query time.

Also many of the 16s entries are not valid names but simply point to another environmental sample?

valid names... hah. For MG-RAST we have them computed against SILVA. to the names are probably as good as it gets.

It would be nice to have though.

THis is one of the areas where a lot of improvement could be made. Better ways of using the pre-computed similarity information e.g. However as good contigs are rare and short reads abound. this has not been where we invested the most energy. Hope this helps Best, Folker

On May 16, 2013, at 3:14 PM, Rick stevens <[email protected]> wrote:

...

For isolate genomes we can use metadata and 16s precomputed mapping.

For WGS and WGS contigs we need to workout precisely what you mean by assign to a taxon grouping.

Sent from my iPad

On May 16, 2013, at 2:58 PM, Rick stevens <[email protected]> wrote:

...

Dylan

I'm trying Ti understand what you want to build.

I think you want some way to have some one select a taxon and bring up in a taxon page all genomes and metagenomes and metagenome derived contigs associated with that taxon..

Is that correct ?

Sent from my iPad

On May 16, 2013, at 2:26 PM, Dylan Chivian <[email protected]> wrote:

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I'm confused. Isn't this week a joint hack-a-thon? My guys flew out there to work with your guys. Is that not happening?

Thanks, - Dylan

On Thu, May 16, 2013 at 12:21 PM, Folker Meyer <[email protected]> wrote: We are super busy right now. Can we do this next week over the phone. I still need some input on the actual goals of this.

-- Sent from mobile device

On May 16, 2013, at 14:14, Matthew Henderson <[email protected]> wrote:

...

Paramvir, Mike and I are at Freund Lodge currently, and you guys (Andreas?) are welcome to come over and be part of the excitement of the KBase build and "stuff". Mike and I will also be here tomorrow morning, but will have to leave around lunchtime to get back to the airport for the trip back home.

Paramvir is less concerned at the moment about thresholding and just wants to see some functionality.

Alternatively, if you are not feeling Freundlich, an email pointing us in the proper direction would also be appreciated.

Thanks, Matt

On Thu, May 16, 2013 at 1:28 PM, Dylan Chivian <[email protected]> wrote: Paramvir is a stakeholder here, so we should get his input, including on which identity thresholds he'd like to see.

Thanks, - Dylan

On Thu, May 16, 2013 at 11:10 AM, Dylan Chivian <[email protected]> wrote: Hi guys,

instead of the call today, probably the time would be best spent with Folker and Andreas working with Matt and Mike directly on the metagenomics species search functionality for the Taxon pages. I expect it is an expensive operation, so it is probably something that should be a one-time compute and stored somewhere associated with each taxon rather than on-the-fly when someone calls up the Taxon page. There should probably also be separate lists for 99% identity and 97% identity (not sure other thresholds make any sense).

Thoughts? Are there other things to discuss and we should have the call anyway?

Thanks, - Dylan

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