Automatic user annotation

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Automatic user annotation

Ferreira, Josie
Hello,

I’m new to WebApollo - I need to generate phylogenetic trees and have a lot of genes to annotate (~30 genes per organism for > 50 organisms) - I’m hoping that WebApollo will be the best way to do this - and hope I don’t need to do it manually.

Is there a way to input a list of sequences with associated gene names that can be BLASTed automatically against all organisms in our WebApollo database and added as a user-annotated feature? We will then be able to pull out all sequences to make trees.

Is this at all possible? I would be grateful to be pointed in the right direction!

Thank you.

Josie






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Re: Automatic user annotation

nathandunn


On Jan 10, 2019, at 4:26 AM, Ferreira, Josie <[hidden email]> wrote:

Hello,

I’m new to WebApollo - I need to generate phylogenetic trees and have a lot of genes to annotate (~30 genes per organism for > 50 organisms) - I’m hoping that WebApollo will be the best way to do this - and hope I don’t need to do it manually.

Well, I think there are many ways to do this and I think there are many ways that Apollo might help, but I don’t think it will be an end-to-end solution for what you’re trying to accomplish.   I’ve seen solutions using Galaxy (https://usegalaxy.org/) and other integrations that solve most of what you’re trying to do. 

Is there a way to input a list of sequences with associated gene names that can be BLASTed automatically against all organisms in our WebApollo database and added as a user-annotated feature? We will then be able to pull out all sequences to make trees.

You can use web services to download the genes / sequences you want (IOServices / write), which mirrors the download method.   Once those are downloaded (examples below):



you can run BLAST and use the hits to indicate hit regions.  

At this point, I would load them as a JBrowse track and manually add them so that you can visually inspect and annotate low quality or equivalent hits.  

If you feel confident in your blast hits, you can add them as user-annotations if you have a way to convert your hits back into confident GFF3s using galaxy, etc..  


You may want to look through here:






Nathan



Is this at all possible? I would be grateful to be pointed in the right direction!

Thank you.

Josie





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