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

[Lincoln Stein]

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.


-- 
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Lincoln D. Stein                           Cold Spring Harbor Laboratory
lstein@cshl.org			                  Cold Spring Harbor, NY

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