[Jalview-discuss] how to select columns by numbers.

Jim Procter jprocter at compbio.dundee.ac.uk
Tue Dec 8 08:24:56 GMT 2009

Hello David.

On 07/12/2009 17:51, David JM wrote:
> 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: 
You can specify a region covering a specific column on the alignment using :

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.


J. B. Procter  (JALVIEW/ENFIN)  Barton Bioinformatics Research Group
Phone/Fax:+44(0)1382 388734/345764  http://www.compbio.dundee.ac.uk
The University of Dundee is a Scottish Registered Charity, No. SC015096.

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