Details
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Type:
Bug
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Status: Resolved
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Priority:
Minor
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Resolution: Fixed
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Affects Version/s: None
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Fix Version/s: 2.5
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Component/s: Feature Request
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Labels:None
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Mantis ID:32893
Description
Can Jalview do this?
Geoff.
---------- Forwarded message ----------
Date: Mon, 19 May 2008 17:50:07 +0200
From: Ioannis Xenarios <ioannis.xenarios@isb-sib.ch>
To: geoff@compbio.dundee.ac.uk
Subject: Jalview for influenza virus multiple alignment
Hello Geoff,
I hope you are doing fine and no I am not coming for the ENFIN project but another cool project I am helping building up and which use heavily Jalview.
I was wondering whether you had within your features for the visualization of multiple alignment a mechanism to ONLY show the differences at each position and render anything that is common with a "-". This is a typical virologist view of different virus segments.
Best
Ioannis
--
****** ADDITIONAL INFORMATION ******
Suggest this is added as a 'colourscheme' where the residue label is changed based on the result of the local (either group or aligment background) conservation analysis of that residue.
There may also be a convention where the mutations are shown relative to a specific consensus (or archetype) sequence which is often shown at the top of the alignment. In that case, the consensus calculation would be w.r.t. that 'archetype' rather than the local residue consensus at that position.
Geoff.
---------- Forwarded message ----------
Date: Mon, 19 May 2008 17:50:07 +0200
From: Ioannis Xenarios <ioannis.xenarios@isb-sib.ch>
To: geoff@compbio.dundee.ac.uk
Subject: Jalview for influenza virus multiple alignment
Hello Geoff,
I hope you are doing fine and no I am not coming for the ENFIN project but another cool project I am helping building up and which use heavily Jalview.
I was wondering whether you had within your features for the visualization of multiple alignment a mechanism to ONLY show the differences at each position and render anything that is common with a "-". This is a typical virologist view of different virus segments.
Best
Ioannis
--
****** ADDITIONAL INFORMATION ******
Suggest this is added as a 'colourscheme' where the residue label is changed based on the result of the local (either group or aligment background) conservation analysis of that residue.
There may also be a convention where the mutations are shown relative to a specific consensus (or archetype) sequence which is often shown at the top of the alignment. In that case, the consensus calculation would be w.r.t. that 'archetype' rather than the local residue consensus at that position.