Re: [Gusdev-gusdev] dots.nalocation table

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

What about an UTR?

Also I have difficulty finding links between the transcript with genefeature.

We have a particular gene described in genefeature view and its
corresponding transcript in dots.transcript.

Sucheta


> in the case of gene, rna and protein, you would use Gene and
> GeneInstance (and similar for RNA, Protein)
>
> Gene and GeneInstance are designed for that.   Gene is the "concept of
> the gene."  GeneInstance links Gene and GeneFeature.  Each "instance"
> represents a "proposal" for what the gene looks like, and what sequence
> it might be found on.
>
> steve
>
> Sucheta Tripathy wrote:
>
>>Steve,
>>
>>I know the way we have been using GUS is slightly different from the way
>>it was meant to be used. In our case, we have a scaffold gets a
>>na_sequence_id which has several features. Now if we are to create
>>different features for a particular gene for different algorithms used,
>>how would link them up together?
>>
>>Sucheta
>>
>>
>>
>>>sucheta-
>>>
>>>i think the way we have generally done this in the past is to add a new
>>>feature, not location, for each algotithm or person that predicts or
>>>edits it.   that is why we have the review and algorithm info on the
>>>feature.
>>>
>>>steve
>>>
>>>Sucheta Tripathy wrote:
>>>
>>>
>>>
>>>>Hi Group,
>>>>
>>>>>From community annotation point of view, I was wondering if it is a
>>>>> good
>>>>idea to have is_reviewed, algorithm_id and reviewer_id in
>>>> dots.nalocation
>>>>table.
>>>>
>>>>Since one na_feature_id( a transcript or a gene) may be having multiple
>>>>sets of nalocations, so one can easily capture them in nalocation with
>>>>different algorithms and with a reviewed option.
>>>>
>>>>In our application we need several gene calling programs to have
>>>>locations
>>>>as well as related information registered.
>>>>
>>>>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