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

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

Hello,

One more question. Does anyone stores the outputs from each gene calling
program e.g; genmark, glimmer, genscan, fgenesh etc.. If yes, which is the
right table for this?

Sucheta

> Take a look at InsertNewExternalSequences, it is quite flexible and may do
> what you want.
>
>                                                  Debbie
>
>
>
>
> On Tue, 18 May 2004, Sucheta Tripathy wrote:
>
>> 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
>> >>
>> >>
>> >>
>> >>
>> >
>>
>>
>>
>
>
>
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-- 
Sucheta Tripathy
Virginia Bioinformatics Institute Phase-I
Washington street.
Virginia Tech.
Blacksburg,VA 24061-0447
phone:(540)231-8138
Fax:  (540) 231-2606