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PomBase website v2
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RNA sequence search widgit #1640

Closed ValWood closed 2 years ago

ValWood commented 3 years ago

To search RNA central (add to RNA pages sequence search section?)

Screen Shot 2020-11-20 at 19 21 32
ValWood commented 3 years ago

consider with https://github.com/pombase/website/issues/39

ValWood commented 3 years ago

This is a widget to search RNA central I think this is an example of it in use at snoDB http://scottgroup.med.usherbrooke.ca/snoDB/sequence_similarity_search/

The button would be added on the RNA pages sequence section here:

Screenshot 2020-12-15 at 20 25 00
ValWood commented 3 years ago

@AntonPetrov can you point us to the complete instructions/source. This was a screengrab from the talk.

AntonPetrov commented 3 years ago

Here you go: https://github.com/RNAcentral/rnacentral-sequence-search-embed

Please let us know if you need any help - @carlosribas or I will be happy to answer any questions.

kimrutherford commented 3 years ago

The button would be added on the RNA pages sequence section here:

Just so I understand, what does the widget do?

ValWood commented 3 years ago

Try the snoDB e.g. http://scottgroup.med.usherbrooke.ca/snoDB/sequence_similarity_search/ (there are some examples).

It searched RNA central, and the output is alignment similar sequences links to expert databases Rfam classification I think also secondary structure prediction, although none of the examples have that.

It might make this unecessary: https://github.com/pombase/website/issues/39

kimrutherford commented 3 years ago

OK, thanks. So we should show the widget in the sequence section, prefilled with the sequence of the RNA?

ValWood commented 3 years ago

yes please. Can it be configured to use our existing prefilled search box (just an additional button for Rfam alongside the other search buttons)?

kimrutherford commented 3 years ago

Hi @AntonPetrov

Is it possible to pre-fill the widget with an RNA sequence when the widget is displayed?

AntonPetrov commented 3 years ago

@kimrutherford Not at the moment, as far as I know.

Just to make sure I understand, you would like to host the RNAcentral search widget somewhere on pombase.org and link to that search page from individual RNAs? I think this would be a very cool way of using the widget!

Carlos is away until January but we can work with him on adding the sequence configuration option when he is back. @carlosribas - this is very similar to what you've done with r2dt-web where the URS can be pre-configured. And we could use it ourselves to restore the "Find similar sequences" button that was removed after the transition to the cloud search.

carlosribas commented 3 years ago

If I understand correctly, @kimrutherford wants to display the widget with an RNA sequence in the search field. Is that right? Whatever the request, I will be happy to work on improving this tool.

ValWood commented 3 years ago

Hi @carlosribas we discussed this yesterday. We decided it would be more consistent to link directly to RNA central as we do with other resources (I think I misunderstood the widget)

ValWood commented 3 years ago

i.e the RNA central search is a bit different , in that it identifies the actual entry rather than our other search options at this point to identify similar sequencess in other organisms.

We will just add the RNA central link tot he external references (we have another ticket for this)

AntonPetrov commented 3 years ago

Thanks @ValWood. Regarding this point:

the RNA central search is a bit different , in that it identifies the actual entry rather than our other search options at this point to identify similar sequences in other organisms

Our search does find similar sequences in other organisms - in addition to the sequence itself. If you choose to search all of RNAcentral, it's conceptually no different than blasting against NCBI or something like that.

ValWood commented 3 years ago

OK, the similarity search will be useful. We will take another look.

ValWood commented 2 years ago

We don't need this search feature as we link to Rfam on a gene by gene basis anyway.