"Show values in textbox" for consensus in Jalview 2.5

Jalview Discussion
1

Hi I have a saved alignement generated from the clustalw service at EMBL-EBI.
When I launch Jalview from the clustalw site - I click on the
consensus and be presented with a "Show values in textbox" option
which then prints to a textbox the following information ( see below).
The second line of this information which indicates the consensus
sequence and the percentage conservation at that point.

This feature is however not available in jalview 2.5 . How can I open
any saved alignment in jalview 2.5 and obtain the consensus
percentage for each position in the alignment for use in another
downstream analysis program.

Thanks
Hari

Show values in textbox" option output:

0.0, 0.0, 0.0, 0.0, 5.4054055, 0.0, 0.0, 5.4054055, 0.0, 0.0, 0.0,
5.4054055, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0,
0.0, 18.918919, 21.621622, 18.918919, 18.918919, 21.621622, 16.216217,
18.918919, 21.621622, 21.621622, 29.72973, 13.513514, 16.216217,
27.027027, 5.4054055, 13.513514, 8.1081085, 10.810811, 13.513514,
16.216217, 24.324324, 48.648647, 13.513514, 0.0, 0.0, 13.513514,
27.027027, 37.837837, 24.324324, 16.216217, 16.216217, 21.621622,
18.918919, 45.945946, 37.837837, 72.97298, 32.432434, 13.513514,
18.918919, 48.648647, 24.324324, 27.027027, 89.189186, 5.4054055, 0.0,
0.0, 0.0, 0.0, 0.0, 35.135136, 40.54054, 62.162163, 29.72973,
37.837837, 78.37838, 21.621622, 18.918919, 35.135136, 45.945946,
24.324324, 0.0, 0.0, 0.0, 24.324324, 16.216217, 32.432434, 83.78378,
16.216217, 24.324324, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0,
0.0, 0.0, 0.0, 21.621622, 18.918919, 29.72973, 45.945946, 18.918919,
24.324324, 72.97298, 21.621622, 18.918919, 45.945946, 29.72973,
24.324324, 13.513514, 91.89189, 51.351353, 18.918919, 16.216217, 0.0,
54.054054, 59.45946, 29.72973, 18.918919, 5.4054055, 29.72973,
40.54054, 16.216217, 16.216217, 32.432434, 21.621622, 21.621622,
54.054054, 16.216217, 16.216217, 0.0, 0.0, 5.4054055, 5.4054055, 0.0,
0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0,
- 0%, - 0%, - 0%, - 0%, M 5%, - 0%, - 0%, I 5%, - 0%, - 0%, - 0%, K
5%, - 0%, - 0%, - 0%, - 0%, - 0%, - 0%, - 0%, - 0%, - 0%, - 0%, - 0%,
- 0%, - 0%, C 18%, L 21%, E 18%, [IV] 18%, [IL] 21%, [KR] 16%, K 18%,
L 21%, K 21%, E 29%, [KN] 13%, D 16%, G 27%, [GS] 5%, R 13%, [RT] 8%,
I 10%, [AS] 13%, K 16%, I 24%, F 48%, [ELP] 13%, - 0%, - 0%, E 13%, L
27%, P 37%, D 24%, R 16%, E 16%, E 21%, V 18%, P 45%, D 37%, Y 72%, Y
32%, K 13%, I 18%, I 48%, K 24%, K 27%, P 89%, G 5%, - 0%, - 0%, - 0%,
- 0%, - 0%, M 35%, D 40%, L 62%, S 29%, T 37%, I 78%, E 21%, Q 18%, K
35%, L 45%, E 24%, - 0%, - 0%, - 0%, S 24%, K 16%, K 32%, Y 83%, K
16%, S 24%, - 0%, - 0%, - 0%, - 0%, - 0%, - 0%, - 0%, - 0%, - 0%, -
0%, - 0%, - 0%, L 21%, A 18%, E 29%, F 45%, E 18%, A 24%, D 72%, [IV]
21%, E 18%, L 45%, [IM] 29%, F 24%, K 13%, N 91%, A 51%, I 18%, R 16%,
- 0%, Y 54%, N 59%, G 29%, K 18%, R 5%, G 29%, S 40%, E 16%, L 16%, Y
32%, K 21%, D 21%, A 54%, [IL] 16%, E 16%, - 0%, - 0%, K 5%, V 5%, -
0%, - 0%, - 0%, - 0%, - 0%, - 0%, - 0%, - 0%, - 0%, - 0%, - 0%,

2

Hello Hari.

I'm sorry about this - its entirely my fault. In my rush to get 2.5 released, I didn't verify that the old CSV output that you need was still possible (my intention was that disabling the sequence logo display would change the annotation mouseover and CSV text, too, but I didn't finish implementing this).

Can you wait until the next release ? I should have time to re-instate the old CSV export style as a bug fix to 2.5 by the end of next week.

Jim.

···

On 13/05/2010 14:21, hari jayaram wrote:

Hi I have a saved alignement generated from the clustalw service at EMBL-EBI.
When I launch Jalview from the clustalw site - I click on the
consensus and be presented with a "Show values in textbox" option
which then prints to a textbox the following information ( see below).
The second line of this information which indicates the consensus
sequence and the percentage conservation at that point.

This feature is however not available in jalview 2.5 . How can I open
any saved alignment in jalview 2.5 and obtain the consensus
percentage for each position in the alignment for use in another
downstream analysis program.

Thanks
Hari

Show values in textbox" option output:

0.0, 0.0, 0.0, 0.0, 5.4054055, 0.0, 0.0, 5.4054055, 0.0, 0.0, 0.0,
5.4054055, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0,
0.0, 18.918919, 21.621622, 18.918919, 18.918919, 21.621622, 16.216217,
18.918919, 21.621622, 21.621622, 29.72973, 13.513514, 16.216217,
27.027027, 5.4054055, 13.513514, 8.1081085, 10.810811, 13.513514,
16.216217, 24.324324, 48.648647, 13.513514, 0.0, 0.0, 13.513514,
27.027027, 37.837837, 24.324324, 16.216217, 16.216217, 21.621622,
18.918919, 45.945946, 37.837837, 72.97298, 32.432434, 13.513514,
18.918919, 48.648647, 24.324324, 27.027027, 89.189186, 5.4054055, 0.0,
0.0, 0.0, 0.0, 0.0, 35.135136, 40.54054, 62.162163, 29.72973,
37.837837, 78.37838, 21.621622, 18.918919, 35.135136, 45.945946,
24.324324, 0.0, 0.0, 0.0, 24.324324, 16.216217, 32.432434, 83.78378,
16.216217, 24.324324, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0,
0.0, 0.0, 0.0, 21.621622, 18.918919, 29.72973, 45.945946, 18.918919,
24.324324, 72.97298, 21.621622, 18.918919, 45.945946, 29.72973,
24.324324, 13.513514, 91.89189, 51.351353, 18.918919, 16.216217, 0.0,
54.054054, 59.45946, 29.72973, 18.918919, 5.4054055, 29.72973,
40.54054, 16.216217, 16.216217, 32.432434, 21.621622, 21.621622,
54.054054, 16.216217, 16.216217, 0.0, 0.0, 5.4054055, 5.4054055, 0.0,
0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0,
- 0%, - 0%, - 0%, - 0%, M 5%, - 0%, - 0%, I 5%, - 0%, - 0%, - 0%, K
5%, - 0%, - 0%, - 0%, - 0%, - 0%, - 0%, - 0%, - 0%, - 0%, - 0%, - 0%,
- 0%, - 0%, C 18%, L 21%, E 18%, [IV] 18%, [IL] 21%, [KR] 16%, K 18%,
L 21%, K 21%, E 29%, [KN] 13%, D 16%, G 27%, [GS] 5%, R 13%, [RT] 8%,
I 10%, [AS] 13%, K 16%, I 24%, F 48%, [ELP] 13%, - 0%, - 0%, E 13%, L
27%, P 37%, D 24%, R 16%, E 16%, E 21%, V 18%, P 45%, D 37%, Y 72%, Y
32%, K 13%, I 18%, I 48%, K 24%, K 27%, P 89%, G 5%, - 0%, - 0%, - 0%,
- 0%, - 0%, M 35%, D 40%, L 62%, S 29%, T 37%, I 78%, E 21%, Q 18%, K
35%, L 45%, E 24%, - 0%, - 0%, - 0%, S 24%, K 16%, K 32%, Y 83%, K
16%, S 24%, - 0%, - 0%, - 0%, - 0%, - 0%, - 0%, - 0%, - 0%, - 0%, -
0%, - 0%, - 0%, L 21%, A 18%, E 29%, F 45%, E 18%, A 24%, D 72%, [IV]
21%, E 18%, L 45%, [IM] 29%, F 24%, K 13%, N 91%, A 51%, I 18%, R 16%,
- 0%, Y 54%, N 59%, G 29%, K 18%, R 5%, G 29%, S 40%, E 16%, L 16%, Y
32%, K 21%, D 21%, A 54%, [IL] 16%, E 16%, - 0%, - 0%, K 5%, V 5%, -
0%, - 0%, - 0%, - 0%, - 0%, - 0%, - 0%, - 0%, - 0%, - 0%, - 0%,
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--
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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.

3

Hi Hari,

···

On 13/05/2010 15:59, Jim Procter wrote:

I'm sorry about this - its entirely my fault. In my rush to get 2.5
released, I didn't verify that the old CSV output that you need was
still possible (my intention was that disabling the sequence logo
display would change the annotation mouseover and CSV text, too, but I
didn't finish implementing this).

Can you wait until the next release ? I should have time to re-instate
the old CSV export style as a bug fix to 2.5 by the end of next week.
   

A little bit later than advertised, but the bug-fix has now been made. The applet now only outputs the simple CSV style, and in the application, the full symbol distribution will only be included in the annotation row's CSV export if the sequence logo is displayed.

Cheers.
Jim.

-----------------------------------------------------------------
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.