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  1. Jalview
  2. JAL-4227

Support Rfam 2020 style per sequence secondary structure lines in stockholm files

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    Details

    • Type: Improvement
    • Status: Open
    • Priority: Major
    • Resolution: Unresolved
    • Affects Version/s: 2.11.2.7, 2.11.3.0, 2.12
    • Fix Version/s: 2.12
    • Component/s: file format issue, na
    • Labels:
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      Description

      Per residue annotation in Rfam releases post 2020 include WUSS lines and other info:

      URS0002311979_119072/1-94 G-GCUUAUCAAGAG-AGG-G-CG-----------------AGGGA--CUGG-CCCGA--CGAC-CCC--CGGCAACC----------AG-------------------------------------------------------AA---------AU--GGUGCCA-AUUC--CUG-CAGCG--------GAA-------
      #=GR URS0002311979_119072/1-94 7EAF_A_SS (.(((((((....(..((.(.....................(((...{{{{.))).........)))..)(((..((..........(....................................................................)..)).)))....(}..}}}.(((((..................


      Binding info:
      #=GC SS_cons (.(((((((,,,,<.<<<.<.--.................-<<<_..AAAA.>>>--..----.>>>.>><<<<-<<.<.<<<._____.......................................................__>....>>>.--..>>>>>>,.,,<a..aaa.<<<<<<_.....____.......
      #=GC RF c.ucUuAUcaAGAG.gGG.c.gG.................AGGGA..cuGG.CCCua..UGAA.gCC.cCgGCAACC.c.ccc.uuuuu.......................................................aag....ggg.Aa..GGUGCcA.AuuC..Cug.Cgggcca.....uaau.......
      #=GC RNA_motif_k_turn ===================X.XX.................XX============XXX..XXXX.X=======================================================================================================================================
      #=GC RNA_ligand_SAM =======X===X=============================================================X=======================================================================================XXX====================================
      #=GC RNA_structural_elements [=P1=5p=][J1][========================P2=============================][======================================P3=variable=SL=========================================][J3][============================P4

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              Assignee:
              Unassigned Unassigned
              Reporter:
              jprocter James Procter
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                Created:
                Updated: