Hi Jim,
Thanks very much for getting back to me so quickly. First, let me thank
you for providing such a well-designed and extraordinarily useful tool. I
very much appreciate the efforts of your group.
Yes, I was aware of the ability to control zoom by adjusting the font, but
this is kind of kludgy and also doesn't allow changes to the spacing
between alignment columns (or compression of the columns - not sure what is
actually happening). I agree that Ctrl+/- would likely work extremely
well, and believe this would also enable zooming by mouse scroll wheel. I
also really like the alignment overview, and think zooming could be
controlled by adjusting the size of the red box in that view.
I actually use Jalview for teaching (CSB472 Computational Genomics &
Bioinformatics), so there are a few features I would love that may not be
frequently requested, but which would be particularly useful when trying to
illustrate different alignment principles. For example, it would be very
nice to be able to extract basic distribution stats and total alignment
score from the conservation and quality related annotation tracks. This
would enable comparison between different alignment. It would also be
helpful to have some other output options for the tract data. For me the
easiest would be if the data were listed vertically (each alignment column
on a separate row). This would make it completely painless to paste into
Excel. Right now it is pretty painful to do this, particularly with a long
alignment.
I think one of the biggest mistakes I make (and certainly my students make)
is when they try to scroll along the sequence using the arrow keys. It was
a real shock to realize that doing this actually shifts the selected
sequence and destroys the alignment. I would very much prefer if this were
not the default behavior. I can't tell you how many alignments I have
screwed up because of this. Can the arrow keys simply move you along the
sequence. Perhaps make shifting the sequence require Shift+arrow. Maybe
there is a simple way to change this behavior that I am not aware of.
Is there a toggle to enable a fixed codon size. IOW, count gaps as position
in the alignment, so a gap in a codon results in a untranslatable amino
acid. This is useful for illustrating the utility of codon-based alignments
(back-translating protein alignments to DNA) as well as why natural
selection generally culls frameshift mutations out of populations.
Is there a way to count the number of stop codons in a sequence or
alignment. Again, not only useful "in the real world", but also useful for
teaching.
When using the Translate to cDNA option, can you please either put the
translation in a tab of the original sequence or put the original sequence
name in the title of the window.
Can the phylogenetic tree be re-rooted or at least default to mid-point
root.
I very often have alignments stall when "Collecting job results". For
example, I have a Muscle alignment stalled right now. It is not
particularly big (60 proteins, ~800aa in length), so I can't understand
where the problem might be. Is there any way to increase the verbosity of
the log data to track these issue better?
That's probably more than you wanted to hear from me. I appreciate your
consideration.
All the best,
David
------------------------------
David S. Guttman
Professor & Associate Chair for Research, Department of Cell & Systems
Biology
Director, Centre for the Analysis of Genome Evolution & Function
University of Toronto
Toronto, Ontario, Canada
Post by Jim ProcterTHanks for the email, David.
Post by David GuttmanIs there an alternative means to zoom in and out of alignments that
doesn't require the middle mouse button? Not all mice have a middle
buttons, and the control on this is poor. This seems like such a
fundamental task that it should be available by other means.
For the moment, you can 'zoom' via the font size menu - since the zoom
is simply implemented as a change in the alignment layout grid size (and
font size change).
We can certainly improve this: it could also be triggered by CTRL/CMD
+/-, as in browsers, or hooked up to mouse clicks via ALT and SHIFT/ALT.
We've also found that a pan/zoom mode is pretty essential when working
with big alignments, including support for trackpad/screen pinch-zoom
gestures. That is planned for a later release in the 2.11 series.
Are there any key combinations you've encountered that would be good for
Jalview to support ?
Jim
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