Remove Redundancy…

Jalview Discussion
1

I have a problem when I attempt to remove redundancy. I select all of my sequences then click Remove Redundancy... The control window comes up set to 100, and no sequences are flagged. But when I decrease the cutoff with the slider, sequences are flagged as they should be, but when I return to 100, sequences are now flagged. I'm not sure which sequences are related by 100%? And if there is any redundancy.

Thanks,
Mark

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_______________________________________________
Mark A. Saper, Ph.D.
Department of Biological Chemistry, University of Michigan Medical School
3040 Chemistry Building | saper@umich.edu | +1 (734) 764-3353

2

Well spotted Mark!

The redundancy looks to have a few redraw problems that I hadn't already lodged in our bug tracker - I've noted them in http://issues.jalview.org/browse/JAL-1340

A couple of points of information that might help:

* redundancy is evaluated based on the current alignment, and percentages are calculated from the perspective of the sequence to be removed. This means that a shorter sequence that is 100% identical at all aligned positions to a longer sequence will be marked for removal.

* a bug in the redundancy slider code means sequences aren't highlighted until after you've touched the slider - although they are marked, and pressing 'Remove' will remove the identical sequences.

* moving the redundancy threshold to 0% marks all sequences for removal - which is technically correct, but not particularly useful, so we'll consider changing that.

There are some odd things that can happen when non-standard symbols are present in the aligned sequences. I'll make a note on the bug so whoever gets to deal with this should take a look...
Jim.

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On 02/07/2013 18:57, Mark Saper wrote:

I have a problem when I attempt to remove redundancy. I select all of my sequences then click Remove Redundancy... The control window comes up set to 100, and no sequences are flagged. But when I decrease the cutoff with the slider, sequences are flagged as they should be, but when I return to 100, sequences are now flagged. I'm not sure which sequences are related by 100%? And if there is any redundancy.

Thanks,
Mark
_______________________________________________
Mark A. Saper, Ph.D.
Department of Biological Chemistry, University of Michigan Medical School
3040 Chemistry Building | saper@umich.edu | +1 (734) 764-3353

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