Integration with GeneValidator.

[yeban]

Hi,

We have developed GeneValidator (GV), a tool to identify potential issues with a gene prediction (Dragan et al, in review). GV does this by comparing CDS or amino-acid sequence of a gene to BLAST hits from the SwissProt or the NR database (configurable). We believe integrating GV with WA might be of interest to the community. Screenshots below (taken from Afra) illustrate how this might work:

Screenshot 1: Right click on a transcript in edit track, select "Send to GeneValidator"

Screenshot 2: Results of validating the transcript's protein products against NR database (loaded in a new window)

This way, GV's report can be used to guide the curation as well as re-assess the quality of gene model after curation. We have implemented a JS API to send sequences from a web page to a GV server for validation. At a higher level this makes integrating GV into WA just a matter of fetching the selected transcripts' protein products and passing them to GV.sendToGeneValidator, with the url of the server and the database to validate against. However, configuration via the xml config file, etc. will have to be considered too, I guess.

[nathandunn]

I would agree . . I think it would be a good integration. We need to think about how to best integrate it within the UI / configuration, but the API makes it look pretty easy.

[cmdcolin]

AnnotTrack's right-click menu is sort of inflexible but I made a new "model" for customizing the right-click menus via #576 which could perhaps make it easier for customizing configurations like this. That's just an idea, it is not added to the AnnotTrack yet

[nathandunn]

@yeban If you want to work on the integration, we'd be happy to work with any pull request you made.

[yeban]

Thanks @nathandunn. I'm home till the end of this month. I will give it a shot after I'm back. I hope that won't be too late.

[nathandunn]

We’ll integrate it in whenever you are done with it (we are constantly releasing). Let us know if you need any help along the way.

Nathan

On Oct 13, 2015, at 3:47 AM, Anurag Priyam [email protected] wrote:

Thanks @nathandunn https://github.com/nathandunn. I'm home till the end of this month. I will give it a shot after I'm back. I hope that won't be too late.

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Reply to this email directly or view it on GitHub #573 (comment).

[monicacecilia]

@yeban @yannickwurm
This is looking really good! Thanks for the update on the progress with GV.

On a related subject, I added an issue for you two at wurmlab/afra#113

[nathandunn]

closing for now. We can re-open if need be.