Hi Fei.
I'm still not absolutely sure what you are after - groups are temporary
in that they're alignment annotation, and the user can delete any
annotation on an alignment view, if they want (of course, you could hack
jalview to disable the 'remove groups' menu option, ..).
What do you need ? Are you interested in highlighting ranges based on
alignment coordinates or according to ranges on specific sequences (e.g.
conserved secondary structure), for instance. Some example data would
help here :)
Jim.
On 11/08/2012 18:46, Fei Cai wrote:
Hi Jim,
Thanks for the suggestion.
"you can create a group on the alignment, which is rendered as a box
around a set of sequences in a range of columns." This box is
temporary right? I want a box that will "highlight" a range (or
multiple boxes for multiple ranges), not really changing the coloring
of alignment. But if the color of the border can be changed that will
be great.
Fei
On Fri, Aug 10, 2012 at 12:57 AM, Jim Procter
<[email protected] <mailto:[email protected]>>
wrote:
On Thu Aug 9 21:30:38 2012, Fei Cai wrote:
Hi all, is there anyway to display DSSP with MSA if one of the
seq has
a known structure (pdb from RCSB or customized pdb)? I tried
Jpred 2nd
structure, but it's way off from the real structure.
There isn't a direct way in v2.7 to run DSSP over the associated
structure to annotate sequences in the alignment, but there is
work in progress that will address this in the next series of
releases. The relevant bug is
http://issues.jalview.org/browse/JAL-674
Also if there a way to highlight or "box" certain range (saying,
alignment position 50-100)?
Not sure what you mean - you can create a group on the alignment,
which is rendered as a box around a set of sequences in a range of
columns.
To create a group interactively, select columns 50-100, right
click on the selected region in the alignment area, follow the
submenus Edit->Group->.. and pick one of the options to create a
group.
Alternately, you could import an annotation file if you are
generating groups from your program. Take a look at the
documentation here:
http://www.jalview.org/help/html/features/annotationsFormat.html
Jim.
--
Fei Cai, Ph.D.
DOE Joint Genome Institute/LBNL Genomics Division
2800 Mitchell Drive, B400-445U,
Walnut Creek, CA 94598-1632, USA
Tel: 925-296-5731 <tel:925-296-5731>
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