RNA secondary structure [sf#88]

[srynobio]

Reported by batchelorc on 2008-02-25 17:56 UTC Hello

(This is all a bit telegraphic.)

This is from October but I haven't got around to doing much about it so trackered so it doesn't evaporate out of my head completely:

Add secondary structure terms (pseudoknot etc.) to sequence_attribute so that, for example, recoding_pseudoknot (SO:0000545) becomes an xp of recoding_stimulatory_region (SO:1001268) with the new pseudoknot quality.

stem_loop becomes a sequence_attribute so that stem loop structures, like SECIS_element (SO:1001274) can inherit that quality.

Colin.

[srynobio]

Updated by eilbeck on 2008-03-28 17:50 UTC

• assigned_to: nobody --> batchelorc

[srynobio]

Commented by eilbeck on 2008-07-09 19:53 UTC Logged In: YES user_id=742851 Originator: NO

So there are pros and cons to this. If these things become attributes then they no longer have a position. So you would not be able to locate the stem loop region. But a lot of these terms are not always continuous regions anyway so it is misleading for them to be where they are.

We could also break up something like pseudoknot into the 2 regions it occupies, the loop and the region it sticks to, and make it a sequence_collection.

??? --KAren

[srynobio]

Commented by batchelorc on 2008-07-11 16:24 UTC Logged In: YES user_id=1473024 Originator: YES

OK. stem_loop_region (SO:new) intersection_of: region, intersection_of: has_quality stem_loop_structure, then SECIS_element has_quality stem_loop_structure and the reasoner does the rest.

Stems, of course, are sequence_collections too. But their definition needs a bit more thought.

Colin.

[srynobio]

Commented by eilbeck on 2009-03-16 21:24 UTC Hi Colin, Are we moving these terms over to RNAO? Should we close this track? --K