Gmod apollo WebGBrowse

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Gmod apollo WebGBrowse

Scooter Willis-2
Gmod apollo WebGBrowse I am in the process of installing GMOD 2.0 and looking for some guidance

We are annotating a fungal genome and have run three different gene prediction algorithms against the scaffold sequences. The users have minimal admin or programming skills so I need to hand them a box that has minimal complexity but will still allow them to use what they need to use. I can output the three prediction results as GFF3 where each would be displayed as a separate track. I also have X% of each predicted protein that has a good hit with other uniprot fungal sequences that I would add as duplicate track with a modified uniprot name to help on the manual annotation process. For the sequences that don’t have hit I would like to add a PFAM track later to assist with the manual annotation. This is my first gmod installation so trying to figure everything out and minimize the amount of time required from making mistakes.

I read through WebGBrowse and looks like that could help speed up the config file process. I have not read the install docs yet so don’t know if they import into a database or read from file once I install WebGBrowse on our server. Also it isn’t clear if you can add new tracks to existing tracks using WebGBrowse by importing a new GFF3 file without the sequence data.

If using apollo for manual annotation does this automatically require storing the data in a chado database? If so is mysql or postgresql recommended?

If somehow, you can point apollo to the gff3 file that is currently being used by gbrowse how are updates captured by gbrowse? My assumption is that both should point to a chado database.

In reading the apollo docs it looks like support for connecting to the database was a once thought about feature but not actively supported/used. Any thoughts on using apollo to connect to a gbrowse 2.0 chado database?

So far I have only installed GMOD 2.0 and just trying to avoid multiple imports as I learn how the various packages work together. Any advice would be greatly appreciated.

Thanks

Scooter

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Re: Gmod apollo WebGBrowse

Ed Lee
Hi Scooter,

> If using apollo for manual annotation does this automatically require
> storing the data in a chado database? If so is mysql or postgresql
> recommended?

Apollo supports a number of formats, but if you want to share the
data with GBrowse, your best bet is to use a Chado backend.
PostgreSQL is the DBMS choice for Chado in GMOD, so you're probably
better off using it as I'd imagine some GMOD Chado tools assumes
PostgreSQL (although from the Apollo side of things, the Chado
support is DBMS agnostic).

> If somehow, you can point apollo to the gff3 file that is currently being
> used by gbrowse how are updates captured by gbrowse? My assumption is that
> both should point to a chado database.

Probably the best approach, although I suppose you could
get them both working through GFF3 files, having a CGI to upload
the curated GFF3s back to the server to be used by GBrowse.

> In reading the apollo docs it looks like support for connecting to the
> database was a once thought about feature but not actively supported/used.
> Any thoughts on using apollo to connect to a gbrowse 2.0 chado database?

I don't think that GBrowse 2.0 requires a special Chado version, so
the default Chado implementation should work for both GBrowse
and Apollo (used to for GBrowser 1.0, at least).

Cheers,
Ed

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