Hello,
I’ve been trying to find out unsuccessfully how to select different columns in a multiple sequence alignment using Jalview, given the column number. I see you can do that easily using the mouse, but I need to do it somehow giving the column numbers by text. My final goal is to select different columns and color them (with same color).
Does anyone know how to do that?
Thank you so much,
David
Hello David.
Hello,
I've been trying to find out unsuccessfully how to select different columns in a multiple sequence alignment using Jalview, given the column number. I see you can do that easily using the mouse, but I need to do it somehow giving the column numbers by text. My final goal is to select different columns and color them (with same color).
I'm not quite sure what you meant 'by text', but it sounds like you might want to colour specific rows automatically when you import the alignment. Perhaps according to some alignment annotation ? There are a few ways you might do this:
1. Define a coloured group over each column on the aligment you want coloured :
Have a look at the annotation file format: http://www.jalview.org/help/html/features/annotationsFormat.html
You can specify a region covering a specific column on the alignment using :
JALVIEW_ANNOTATION
SEQUENCE_GROUP Group_A 55 55 *
PROPERTIES Group_A colour=0xFF0000
(note - the spaces in the line above have to be changed to a single tab character before this will work).
Importing this will colour the 55'th column red. To colour multiple columns, you need to specify a group for each column, and give each one a unique name (at the moment, jalview will only apply the properties specified in the 'properties' line to the first group with a given name, rather than all of them).
2. Define an annotation row and use the 'colour by annotation' function from the colour menu:
You can use the annotation file above to create an annotation row with values at specific column positions. You can then use the 'Colour by Annotation' dialog to shade the alignment using the annotation row (try it with the annotation in the example feredoxin alignment).
Again, there are deficiencies in the current version of jalview for this: there is currently no way to set the 'colour by annotation' function automatically - but I am in the progress of extending the annotation file format to enable this kind of colour setting specification.
Do any of the above achieve what you are asking ? Apologies if I've misunderstood what you meant to do!
Jim Procter.
On 07/12/2009 17:51, David JM wrote:
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