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

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

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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