Dear all,
When I work with MSAs that contain large gaps, I encounter the following problem when I try to remove redundancy: it tells me that all sequences except the top one are redundant (90%) although I know for a fact that they are not all redundant. Did any of you encounter this problem? if so, how do you fix it?
Thank you ,
Doran Hendin-Barak
Hi Doran. Sorry for the late reply ...
When I work with MSAs that contain large gaps, I encounter the
following problem when I try to remove redundancy: it tells me that
all sequences except the top one are redundant (90%) although I know
for a fact that they are not all redundant. Did any of you encounter
this problem? if so, how do you fix it?
What is happening is that Jalview uses the alignment to calculate percentage identity between the sequences. This means that if there are no mutations, all the sequences are considered identical. If you want to remove redundant sequences from a set, then you should first use the 'Remove all gaps' function, and then try the redundancy filter again.
I lodged a feature request about this last year, but haven't managed to get around to implementing it yet: http://issues.jalview.org/browse/JAL-743
Jim.
On 05/03/2012 11:52, doranhen@post.tau.ac.il wrote: