GFF3 question

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GFF3 question

Sofia Robb
Hello,

I use my GFF3 with gmod_bulk_load.pl.

If I want to add sequences to my gff3 I know that I can add the
following to the bottom of my GFF3 file.

##fasta
 >seq1
 >seq2

My question is, what do the >seq1 and >seq2 need to correspond to in the
GFF3 file?  can it be ID=, or does it have to be Target= as is seen in
the documentation?

Also, is there a Tag that i can add to the last column of the gff in
which I can indicate short sequences as Values which will end up in
residues field in the feature table?

Thanks,
Sofia

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Re: GFF3 question

Scott Cain-2
(also cc'ed to the schema list, which has a much larger reader base.)

Hi Sophia,

Sorry for the delay; I just got back from an extended trip to through
the Carolinas :-)

The sequence identifiers can definitely correspond to ID tags, since
that is how I typically load chromosome sequences.  It should also work
for Target tags too, though I don't recall testing that off the top of
my head.

About your last question, the short answer is no.  Why wouldn't you put
that in the fasta section?

Scott

On Wed, 2006-07-05 at 16:27 -0600, Sofia Robb wrote:

> Hello,
>
> I use my GFF3 with gmod_bulk_load.pl.
>
> If I want to add sequences to my gff3 I know that I can add the
> following to the bottom of my GFF3 file.
>
> ##fasta
>  >seq1
>  >seq2
>
> My question is, what do the >seq1 and >seq2 need to correspond to in the
> GFF3 file?  can it be ID=, or does it have to be Target= as is seen in
> the documentation?
>
> Also, is there a Tag that i can add to the last column of the gff in
> which I can indicate short sequences as Values which will end up in
> residues field in the feature table?
>
> Thanks,
> Sofia
>
> Using Tomcat but need to do more? Need to support web services, security?
> Get stuff done quickly with pre-integrated technology to make your job easier
> Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo
> http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642
> _______________________________________________
> Gmod-chado-seq-ad mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-chado-seq-ad
--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                         [hidden email]
GMOD Coordinator (http://www.gmod.org/)                     216-392-3087
Cold Spring Harbor Laboratory


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