about chado

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about chado

Marcelo Goncalves Narciso (Pesquisador)
Hi people,
good morning.

I need to send data from rice SNPs (.gff3 file) and
I try the command

 sudo /usr/local/bin/gmod_bulk_load_gff3.pl --dbname chadodb --dbuser uuu
--dbpass xxxx --dbhost localhost --organism  --gff riceVariety.gff3

I would like to know if I have download archives .gbk from
NCBI about OryzaSativa and transform it in .gff3 and load in the
bank.

How to send data from SNP and rice to chado and how I
use Gbrowser with chado is my question.

Thank you.

Marcelo.
--
Embrapa Arroz e Feijao (http://www.cnpaf.embrapa.br)


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Re: [Gmod-help] about chado

Scott Cain
Hi Marcelo,

I'm cc'ing this to the schema mailing list; the help and devel mailing
lists can be removed from follow up messages.

If I understand you correctly, you already have a GFF3 file of rice
SNPs that you obtained by converting a GenBank file to GFF3, and you'd
like to load that into Chado and browse with GBrowse, is that right?
While you can do that, the question I have is, do you already have a
Chado database with rice data in it?  I don't know anything about the
rice data set, but I imagine it would be quite big, and I'm not sure
what you'd gain from putting it in Chado.  If you only want to browse
it in GBrowse, it would probably make more sense to put the data in a
Bio::DB::SeqFeature::Store database (using the bp_seqfeature_load.pl
script that comes with BioPerl).

Scott


On Fri, Oct 29, 2010 at 11:29 AM, Marcelo Goncalves Narciso
(Pesquisador) <[hidden email]> wrote:

> Hi people,
> good morning.
>
> I need to send data from rice SNPs (.gff3 file) and
> I try the command
>
>  sudo /usr/local/bin/gmod_bulk_load_gff3.pl --dbname chadodb --dbuser uuu
> --dbpass xxxx --dbhost localhost --organism  --gff riceVariety.gff3
>
> I would like to know if I have download archives .gbk from
> NCBI about OryzaSativa and transform it in .gff3 and load in the
> bank.
>
> How to send data from SNP and rice to chado and how I
> use Gbrowser with chado is my question.
>
> Thank you.
>
> Marcelo.
> --
> Embrapa Arroz e Feijao (http://www.cnpaf.embrapa.br)
>
>



--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

------------------------------------------------------------------------------
Nokia and AT&T present the 2010 Calling All Innovators-North America contest
Create new apps & games for the Nokia N8 for consumers in  U.S. and Canada
$10 million total in prizes - $4M cash, 500 devices, nearly $6M in marketing
Develop with Nokia Qt SDK, Web Runtime, or Java and Publish to Ovi Store
http://p.sf.net/sfu/nokia-dev2dev
_______________________________________________
Gmod-devel mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-devel