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

[Bindu G. <bi...@pc...>]

hi Sucheta -
Sorry to say, but we do not have a plugin that is ready to use.
we use the plugin:  ImportPlasmoDBAAFeatures.pm
however, i must warn you that this is a in-house plugin, which is very
specific to plasmodium data, and not free from hard-coded values.
it takes tab-delimited text input i believe. also, this plugin has gone
further iterations since the last commit to sanger cvs.

Bindu


On May 20, 2004, at 8:02 AM, Sucheta Tripathy wrote:

> 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