[Gmod-help] Loading sequences with no GI in chado

[Scott Cain]

Or, would it be possible to add text to it to make it look more like a
GenBank file so the BioPerl parser would be able to work with it?


On Fri, Sep 25, 2009 at 9:16 AM, Scott Cain <scott at scottcain.net> wrote:
> Hi Paul,
>
> So what you have is files formatted like GenBank files, but not actual
> GenBank files?  Where did the data come from?  If converting those
> isn't working properly, it is really a BioPerl problem (though still
> ultimately our problem :-)
>
> What does happen?  Would it be possible to go back to the originator
> of this file to get it in some other format?
>
> Scott
>
>
>
>
> On Fri, Sep 25, 2009 at 2:06 AM, Paul Visendi <P.Visendi at cgiar.org> wrote:
>> Halo Help desk,
>>
>> We at the International Livestock Research Institute have sequenced a strain
>> of Theileria parva .
>>
>> we have set up chado on postgresql and we are trying to store this sequence
>> information in the chado schema.
>>
>> converting this sequence files to GFF3 has been a problem. How can this be
>> done since the files we  have are in genbank format without accession
>> numbers, GI identifiers etc
>>
>> only the features section exists
>>
>> Thank you in advance,
>>
>> visendi
>>
>
>
>
> --
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at scottcain dot net
> GMOD Coordinator (http://gmod.org/)                     216-392-3087
> Ontario Institute for Cancer Research
>



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