[Bioperl-l] arabidopsis + load_seqdatabase.pl

Angshu Kar angshu96 at gmail.com
Tue Dec 20 00:12:01 EST 2005


Arabidopsis is the datasource on which we need to work upon. Thats why i
need to load all arabidopsis info into the biosql schema.

Thanks for your info.


On 12/19/05, Sean Davis <sdavis2 at mail.nih.gov> wrote:
> On 12/19/05 5:39 PM, "Angshu Kar" <angshu96 at gmail.com> wrote:
> > Sean,
> >
> > I've tried .faa, .fna and .gbk files in the link mentioned below. After
> > running the script when I saw the loaded database, I saw that in the
> bioentry
> > table the 3 fields accession, identifier and name containing the same
> > data.Also, the version column was not populated. I want them to be
> correctly
> > parsed. So I want an arabidopsis data file that "goes well" with the
> > load_seqdatabase.pl script.
> I would suggest reading the NCBI handbook on genbank format files and then
> look at and go through the exercises here:
> http://bioperl.org/HOWTOs/html/Feature-Annotation.html
> Do this with your genbank file of interest and see where things end
> up.  My
> guess is that all the things that you think of as sequences end up as
> sequence features--look at the genbank file.  That is probably (though I'm
> not sure) where the answer is.
> Again, why do you want these information in a biosql database?  Just
> curious....  There may be a much easier way to go about what you want to
> do,
> but I can't be sure.
> Sean

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