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PomBase website v2
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New commonly used query: RNA genes with predicted 2D structures #2187

Closed kimrutherford closed 3 months ago

kimrutherford commented 3 months ago

@ValWood We have "Proteins with PDB structures". Should we add something similar for RNA structures?

ValWood commented 3 months ago

`That would be nice, it's diffiuclt to know which ones have secondary structures

We should call it "RNA secondary structure predictions"

kimrutherford commented 3 months ago

That's done for Saturday morning. It needs a nightly load and I didn't push the changes in time.

kimrutherford commented 3 months ago

https://github.com/pombase/website/issues/1989#issuecomment-1926720128

Try to embed as a widget on the tRNA, snRNA, snoRNA and rRNA pages

The list of RNA genes produced by the new query includes some RNA types that aren't in your list: lots of lncRNAs and one sncRNA (SPNCRNA.463). Here's the full list that will be the new query tomorrow: https://www.pombase.org/results/from/id/68cd3116-9daa-40be-8ece-0a62cc6f2964

Should we show the 2D structure widget on those lncRNA pages?

Most of them don't look useful but there are some that fold sensibly: https://rnacentral.org/rna/URS000230DC2B/4896 https://www.pombase.org/gene/SPNCRNA.6405

The one sncRNA with a predicted structure (SPNCRNA.463) doesn't look great: https://rnacentral.org/rna/URS00003E9371/4896

ValWood commented 3 months ago

Most of them don't look useful but there are some that fold sensibly: https://rnacentral.org/rna/URS000230DC2B/4896 https://www.pombase.org/gene/SPNCRNA.6405

blimey that's a tRNA embedded in a lncRNA, I will take a look at that!

kimrutherford commented 3 months ago

blimey that's a tRNA embedded in a lncRNA, I will take a look at that!

There are a bunch of other lncRNA genes that look similar:

SPNCRNA.7042 - https://rnacentral.org/rna/URS000230D4B2/4896 SPNCRNA.7125 - https://rnacentral.org/rna/URS000230D734/4896 SPNCRNA.7383 - https://rnacentral.org/rna/URS000230DD31/4896 SPNCRNA.7463 - https://rnacentral.org/rna/URS000230DE76/4896 SPNCRNA.2529 - https://rnacentral.org/rna/URS000230DC70/4896 SPNCRNA.1669 - https://rnacentral.org/rna/URS000019CED9/4896 SPNCRNA.2479 - https://rnacentral.org/rna/URS000230D749/4896 SPNCRNA.2656 - https://rnacentral.org/rna/URS000230D399/4896 SPNCRNA.2777 - https://rnacentral.org/rna/URS000230DE13/4896 SPNCRNA.2990 - https://rnacentral.org/rna/URS000230E2E9/4896 SPNCRNA.3131 - https://rnacentral.org/rna/URS000230DDBA/4896 SPNCRNA.4841 - https://rnacentral.org/rna/URS000230D36A/4896

And one that RNAcentral lists as 5S ribosomal RNA: SPNCRNA.4731 - https://rnacentral.org/rna/URS000230E3F3/4896

kimrutherford commented 3 months ago

blimey that's a tRNA embedded in a lncRNA, I will take a look at that!

Moved to:

That's done for Saturday morning. It needs a nightly load and I didn't push the changes in time.

That's available now.

Should we show the 2D structure widget on those lncRNA pages?

Maybe we can discuss this on the next call.

ValWood commented 3 months ago

yes show them, they should all be fixed eeventually

kimrutherford commented 3 months ago

OK. This can be closed then.