I see that JalView can color code each residue according to the Percentage Identity relative to that column. Is there a way to output the overall percentage identity for each column?
Hi.
I see that JalView can color code each residue according to the Percentage Identity relative to that column. Is there a way to output the overall percentage identity for each column?
There certainly is. The overall percentage identity is given in the Consensus histogram at the bottom of the alignment plot (assuming you've got 'Show annotations' ticked in the View menu). Right-clicking the 'consensus' label gives you a pop-up menu including an option allowing you to export the annotation as comma separated values (note: if you have sequence logos displayed then you'll get all symbol percentages, rather than just the one(s) with the greatest share).
Does that answer your question ?
Jim.
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On 13/07/2011 18:14, wormbuff wrote:
Perfect! I didn't realize that this was considered an annotation. Thank you very much.
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On Jul 13, 2011, at 10:43 AM, Jim Procter wrote:
Hi.
On 13/07/2011 18:14, wormbuff wrote:
I see that JalView can color code each residue according to the Percentage Identity relative to that column. Is there a way to output the overall percentage identity for each column?
There certainly is. The overall percentage identity is given in the
Consensus histogram at the bottom of the alignment plot (assuming you've
got 'Show annotations' ticked in the View menu). Right-clicking the
'consensus' label gives you a pop-up menu including an option allowing
you to export the annotation as comma separated values (note: if you
have sequence logos displayed then you'll get all symbol percentages,
rather than just the one(s) with the greatest share).Does that answer your question ?
Jim.
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