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  1. Jalview
  2. JAL-1018

create row showing conserved physicochemical properties

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    Details

    • Type: New Feature
    • Status: Open
    • Priority: Major
    • Resolution: Unresolved
    • Affects Version/s: None
    • Fix Version/s: None
    • Component/s: None

      Description

      Create a row with the conserved physico-chemical conservations outlined, as in Promals3D (the simple version of Promals doesn't do it). I can send you an example of their output if you wish when I'm back in my lab next week ; but basically they say "polar" if at a given position there's more than x% of DQENSTHN, small if it's A or G or S or V, tiny if it's AGS, etc and put it in bold if it's perfectly conserved (you already have a star for that). It's obviously very useful to check alignments or for mutational analyses - especially for beginners, and even for advanced bioinformaticians it's still faster than to try and compute it by oneself. Obviously the choice of small, hydrophobic etc can be arbitrary, but why not take the one of Promals3D or ask them why they've chosen it. Seems to work for me.

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            Assignee:
            jprocter James Procter
            Reporter:
            dkarlin773 David Karlin
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              Created:
              Updated: