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  1. Jalview
  2. JAL-4070

grokking relative positions of features on an alignment

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    Details

    • Type: Story
    • Status: Open
    • Priority: Major
    • Resolution: Unresolved
    • Affects Version/s: None
    • Fix Version/s: 2.11.3, 2.12
    • Component/s: None
    • Labels:
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      Description

      It's often extremely useful to get an idea of where particular types of feature appear w.r.t. to each other in an alignment. For a small alignment this is easy to do visually, but for large alignments, it's more convenient to analyse feature positions for sequences as they appear in each column.

      Jalview provides a way to do this via sequence feature based trees, but these can be hard to interpret. Other useful approaches are:
      1. Simply export each feature's position on the alignment - so they can be visualised with another tool.
      2. Right click on the feature's type in the Feature Settings dialog and apply the 'Hide columns not containing feature' option.
      3. Use JAL-4061 & JAL-4062 to Find the features of interest, select and copy/paste them to a new alignment. This allows them to be 'aligned' independently of their context, and then subsequently shown in context view the 'view flanking alignment' operation under Calculations.
      4. Apply the visibleFeaturesCounter groovy script - which implicitly shows the extent of features of a particular type.

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