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ebi-webcomponents / protvista-uniprot

The ProtVista tool for the UniProt website
MIT License
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Information for Isoforms #14

Open AurelieMLB opened 4 years ago

AurelieMLB commented 4 years ago

Hello,

Is it possible to call provista to get the annotations based on an isoform sequence please? e.g.: https://www.uniprot.org/uniprot/P00533/protvista But https://www.uniprot.org/uniprot/P00533-2/protvista Does not seem to work. I understand that the annotations are classically based on the most representative isoform but sometimes it is valuable to visualise those on the isoform of interest. Alternatively, is there a way to submit a sequence? Or load data from a local file rather than loading data directly from Uniprot please? Is anything like this planned please? Where is the sequence pulled from please?

Many thanks

xwatkins commented 4 years ago

Hi Aurelie,

AurelieMLB commented 4 years ago

Hello,

Thanks for your reply!

I would need to display information for some specific isoform sequence (one at a time). As this is not yet there, I was thinking about looking for isoform specific info and also transpose general information from the main isoform after alignment. I would then generate local files in the same format as the EBI protein API does. Finally I was hoping being able to use this (these) local file(s) with specific sequence and well fomatted info directly in Protvista locally. Am I making sense?

Basically, I would like to use Protvista for local data. Would this be at all possible please?

Many thanks

On Thu, 23 Apr 2020, 16:36 Xavier Watkins, notifications@github.com wrote:

Hi Aurelie,

  • Protvista currently uses the EBI Proteins API https://www.ebi.ac.uk/proteins/api/doc/ to load all its data (sequence and features), and the feature information is not isoform-specific (so isoform features will be displayed on the canonical). However, as we work on the new UniProt website we will have isoform-specific annotation available, and we are planning on being able to view isoform & canonical sequences and features in the same ProtVista. This is however still at the planning stage.
  • There are ways to display your own data in ProtVista, what format is your data in?
  • What do you mean by "submit a sequence"? Do you mean to be added in UniProt?

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