Re: [Gusdev-gusdev] amino acid data upload to GUS

[Sucheta T. <su...@vb...>]

Hi Debbie,

We have protein data after using the gene calls. These are present in raw
fasta format. To these sequences we did the signalP analysis and other
annotation. I saw the table format and we can easily parse them onto the
column names, but I was wondering before that I need to put them onto
aasequenceImp table. So I thought if I can put my raw protein sequences to
the table with some plugin.

Thanks

Sucheta
> Hi Sucheta,
>
>
> What is the data that you want to load? It is hard to answer the question
> generally.
>
> As you probably know already we load data from the protein nr database
> files from NCBI and protein motif data from prodom and cdd. Those are
> loaded with LoadNRDB.pm (written specifically for NCBI nrdb protein data)
> and InsertNewExternalSequences.
>
> We also load signal peptide and transmembrane results from the analysis
> of our assemblies. Those plugins are not in cvs repository at Sanger and
> may not be appropriate for your use.
>
>                                                         Debbie
> On Tue, 18 May 2004, Sucheta Tripathy
> wrote:
>
>>
>> Hello All,
>>
>> Has anyone tried uploading amino acid related data to GUS(mainly to
>> aasequenceImp  and related tables). Is there a plugin for that? I have
>> lots of amino acid related data like the signalP output and other
>> annotations.
>>
>> Any suggestions?
>>
>> Thanks
>>
>> Sucheta
>>
>>
>>
>>
>


-- 
Sucheta Tripathy
Virginia Bioinformatics Institute Phase-I
Washington street.
Virginia Tech.
Blacksburg,VA 24061-0447
phone:(540)231-8138
Fax:  (540) 231-2606