Hi Oliver -
Thanks for perservering with posting your feature request on our bug-tracker (https://issues.jalview.org/browse/JAL-3237) ! We have fairly strict size limits on the email discussion list, so your email didn’t make it to the list, but I’ve included the text below so other members can see what you asked.
I’m a structural biologist, and I find Jalview extremely useful for making annotated protein sequence alignments!
There is one feature that I would really love though: I would like to be able to have the upper scale ignore gaps. That is, to have the upper scale reflect the sequence numbering of a specified reference sequence, rather than the alignment position. This is very useful when cross-referencing with a structure, so I can quickly check from an alignment figure which particularly interesting residue is which numbering in a structure.
Currently I do this manually in a vector graphics program (see below), which becomes rather tedious when one is dealing with an alignment of 5000 residue protein sequences
Jalview can already do some of what you ask - if you open the sequence ID popup menu for the sequence that you’d like to define as a reference by right-clicking it’s label, select the ‘Set as Reference’ in the submenu with the same name as the label, then the alignment ruler will now be numbered according to that sequence.
See here for more info:
http://www.jalview.org/help/html/calculations/referenceseq.html
The only other thing I would love is the ability to add custom, editable secondary structure annotations at the bottom of the alignment, although I realize that might be a bit of a tricky one… I’d love to be able to highlight a region of sequence and define as beta sheet, alpha helix, coil or disordered via a context menu and then have that appear as an annotation layer below the sequence.
You can also interactively create annotation on the alignment (see https://www.youtube.com/watch?v=W3ZocfWqS_s and http://www.jalview.org/help/html/features/annotation.html ). If you haven’t already then make sure you have enabled the ‘Process Secondary Structure’ option in Jalview’s Structure preferences, since that will automatically annotate sequences with DSSP 3-state labels from their associated 3D structure (which I’m sure you’ve already discovered how to do via the View 3D Structure’ popup menu).
Of course, what we are missing is a ‘disordered’ annotation label (Jalview already offers alpha and beta). I’ve already created a feature request at https://issues.jalview.org/browse/JAL-3238 - let us know how you would normally highlight a disordered region and we’ll see what we can do.
Keep up the good work, Jalview is a wonderful and essential piece of software!
Thanks very much!
Jim.
PS. Watch out for an announcement this week about how to try out the next Jalview release, which we are just about to beta test at our Edinburgh Genomics Jalview training course tomorrow.
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On 27/04/2019 18:37, Oliver Clarke wrote:
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Dr JB Procter, Jalview Coordinator, The Barton Group
Division of Computational Biology, School of Life Sciences
University of Dundee, Dundee DD1 5EH, UK.
+44 1382 388734 | [www.jalview.org](http://www.jalview.org) | [www.compbio.dundee.ac.uk](http://www.compbio.dundee.ac.uk)