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  1. Jalview
  2. JAL-3237

Show numbering of reference sequence in upper scale and interactive secondary structure/disorder annotation



    • Type: Story
    • Status: In Progress
    • Priority: Major
    • Resolution: Unresolved
    • Affects Version/s: 2.11.0
    • Fix Version/s: 2.11.1
    • Component/s: annotation, Structures
    • Labels:



      I'm a structural biologist, and I find Jalview extremely useful for making annotated protein sequence alignments!

      There is one feature that I would really love though: I would like to be able to have the upper scale ignore gaps. That is, to have the upper scale reflect the sequence numbering of a specified reference sequence, rather than the alignment position. This is very useful when cross-referencing with a structure, so I can quickly check from an alignment figure which particularly interesting residue is which numbering in a structure.

      Currently I do this manually in a vector graphics program (see below), which becomes rather tedious when one is dealing with an alignment of 5000 residue protein sequences :)

      The only other thing I would love is the ability to add custom, editable secondary structure annotations at the bottom of the alignment, although I realize that might be a bit of a tricky one... I'd love to be able to highlight a region of sequence and define as beta sheet, alpha helix, coil or disordered via a context menu and then have that appear as an annotation layer below the sequence.

      Keep up the good work, Jalview is a wonderful and essential piece of software!

      Oliver Clarke (Columbia University, NY)

      PS: (Wasn't sure where to post this - I tried posting to jalview-discuss but I don't think it went through.)


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        3. Screen Shot 2019-04-28 at 11.39.51 AM.png
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        6. Screen Shot 2019-04-29 at 9.32.09 AM.png
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          Oliver Clarke

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              jprocter James Procter
              olibclarke Oliver Clarke
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