Information for Isoforms

[AurelieMLB]

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]

Hi Aurelie,

• Protvista currently uses the EBI Proteins API 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?

[AurelieMLB]

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, ***@***.***> 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? — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#14 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ADA3XY2DBSA5P5ZZDOI2HETROBOABANCNFSM4MOHFXIA> .