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

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

Hi Bindu,

Thanks, Do you use any plugin for this or you do direct upload.

Sucheta

> HI Sucheta -
> We load glimmer, phat and genefinder predictions of plasmodium in
> dots.GeneFeature.
>
> Bindu
>
>
> On May 19, 2004, at 4:46 PM, Sucheta Tripathy wrote:
>
>> 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
>>
>>
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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