[Bioperl-l] Re: Gadfly in gbrowse (Bio::Graphics + Bio::DB::GFF)

[Chris Mungall]

Wow, this is fantastic Lincoln.

(internal note to flydev: we should install Bio::DB::GFF ASAP, and use it
as a denormalized gadfly underneath our seqviews)

The worm->gadfly is looking pretty shoddy right now but we'll have
something decent up soon...

On Wed, 21 Nov 2001, Lincoln Stein wrote:

> Hi,
> 
> It took a few hours of scripting to massage the Gadfly "Pseudo-GFF"
> files into something suitable for loading into Bio::DB::GFF, but I now
> have the Gadfly Drosophila annotations running in the MODules genome
> browser.  No changes to the database or browser were needed.  So now
> we've got a Fly->Worm brain transplant!
> 
> To see it, go to http://www.wormbase.org/db/seq/gbrowse, and select
> "Drosophila Release 2" from the popup menu near the bottom.
> 
> Type in:
> 
>      - A chromosome arm, such as 2L
>      - A scaffold name, such as AE003652
>      - A BAC name, such as BACR25J11-TET3
>      - A gene ID, in the format Gene:CG9138
>      - A transcript ID, in the format Transcript:CT26172
> 
> Objects link back to Gadfly, but I don't know all the link rules, so
> some things work (like transcripts) and other things don't (like
> clones).
> 
> The FastA dumps don't work at the moment because I don't have the
> Drosophila sequence installed.
> 
> Lincoln
> 
> PS: I'm going to add the Perl script that converts the Gadfly GFF
> files into the "right" GFF format to the Bio::DB::GFF distribution.
> 
> 
> -- 
> ========================================================================
> Lincoln D. Stein                           Cold Spring Harbor Laboratory
> lstein@cshl.org			                  Cold Spring Harbor, NY
> 
> NOW HIRING BIOINFORMATICS POSTDOCTORAL FELLOWS AND PROGRAMMERS. 
> PLEASE WRITE FOR DETAILS.
> ========================================================================
>