Details
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Type:
Story
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Status: Open
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Priority:
Major
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Resolution: Unresolved
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Affects Version/s: 2.11.4.0
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Fix Version/s: 2.11.5.0
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Component/s: analysis, Structures
Description
The SIMSApiper (https://academic.oup.com/bioinformatics/article/40/5/btae276/7656375?login=false) publication includes a few good examples of sequences with structures:
https://github.com/Bio2Byte/simsapiper/blob/main/data_manuscript/TIM_barrels.zip
In Jalview 2.11.4.0 one of the alignments can be loaded in, then all the structures can be added by selecting them and drag/dropping them on to the MSA.
Association is quite fast - no progress bar is shown though, and then the 'Add Reference Annotation' option becomes available.
- secondary structure is added
- structures are not autodetected as alphafold models - so the provider assignment is 'Structure', and the PLDDT is shown as temperature factor.
Once imported:
- consensus secondary structure reflects structural conservation
- filter by occupancy allows columns to be selected -> tree calculation to look at conservation of secondary structure.
---> problem here is need to remember to hide columns before calculating tree. Ideally calculation dialog should indicate what part of the alignment view is going to be used, or at least provide option to use selected columns only.
- group consensus and ss-consensus should be useful to navigate - but need to be able to sort group-associated rows by type (JAL-4386 will make this easier with the secondary structure colours, but still not sufficient ).
https://github.com/Bio2Byte/simsapiper/blob/main/data_manuscript/TIM_barrels.zip
In Jalview 2.11.4.0 one of the alignments can be loaded in, then all the structures can be added by selecting them and drag/dropping them on to the MSA.
Association is quite fast - no progress bar is shown though, and then the 'Add Reference Annotation' option becomes available.
- secondary structure is added
- structures are not autodetected as alphafold models - so the provider assignment is 'Structure', and the PLDDT is shown as temperature factor.
Once imported:
- consensus secondary structure reflects structural conservation
- filter by occupancy allows columns to be selected -> tree calculation to look at conservation of secondary structure.
---> problem here is need to remember to hide columns before calculating tree. Ideally calculation dialog should indicate what part of the alignment view is going to be used, or at least provide option to use selected columns only.
- group consensus and ss-consensus should be useful to navigate - but need to be able to sort group-associated rows by type (JAL-4386 will make this easier with the secondary structure colours, but still not sufficient ).