Re: [Gmod-gbrowse] Genebank to GMOD help

[Dave M. <mat...@gr...>]

Hi Dan,  I've been trying to get Genbank records into GBrowse too.  So far
with the same result, "landmark not recognized".  Current state is at
http://ceres.plbr.cornell.edu/cgi-bin/gbrowse/MBovis

"landmark not recognized" is GBrowse's horror, too many things can cause it.
Some things to help eliminate:

- I'm using the in-memory database and the directory has the permissions
  prescribed in docs/pod/GENBANK_HOWTO.pod.
  ("chmod o+rwx"??  Is write permission needed?  I did it anyway.)

- I used bp_genbank2gff.pl from bioperl-1.5.0.  It's dated 2004/05/05.
  Using GBrowse 1.62.

- The supplied databases/yeast_chr1/chromosome1.gff file works fine with the
  in-memory adapter.

Looking at the gff file produced by bp_genbank2gff.pl, it sure isn't 
very much like the yeast example or like the description of the GFF 
information GBrowse wants that's given in CONFIGURE_HOWTO.  I tried 
tinkering with file to make it look more reasonable, but never got 
GBrowse to read it.

The only partial success I've had so far was by using a different script,
bp_genbank2gff3, (bioperl-1.5.0/blib/script/bp_genbank2gff3.pl).  This one
was able to convert a different GenBank record, AY663391, to a GFF that
GBrowse reads fine.  However its GFF output from the M. bovis record
NC_002945 also fails to work.

There are a lot of differences in the output from bp_genbank2gff and
bp_genbank2gff3.  Hard to tell which are important, if any.

- Dave

> From: "Dan Cardin" <ft...@ua...>
> Subject: [Gmod-gbrowse] Genebank to GMOD help
> Date: Wed, 16 Feb 2005 16:15:26 -0900 (AKST)
> 
> Hello, I am trying to take a sequence I downloaded from genbank and
> display it through. I keep getting an error saying "The landmark named
> AJ749949 is not recognized. See the help pages for suggestions."
> 
> I am dead in the water. I ran bp_genbank2gff and put the files in the
> appropiate directories, changed permissions. Setup the config file. I
> tried to follow the example given as best as I could. I even did the
> example given verbatim and I recieved the same error. Any help would be
> great. Thank you
> -dc

-   -   -   -   -   -   -   -   -   -   -   -   -   -   -   -   -   -   -   -
David E. Matthews, Ph.D.          USDA-ARS Plant Genome Database Curator
Cornell University                Email: mat...@gr...
Department of Plant Breeding                          Phone: +1-607-255-9951 
409 Bradfield Hall                                      Fax: +1-607-255-6683
Ithaca, New York 14853, USA             GrainGenes: http://wheat.pw.usda.gov