secondary structure annotation

Jalview Discussion
1

Hi-

I am getting strange results for my secondary structure in a pairwise alignment using the jalview applet:

http://pdbjc01.protein.osaka-u.ac.jp:8888/tmp/SS32349/3bknmodA_PDP_A_1jgcC_SCOP_A_applet.html

The secondary structure is supposed to correspond to the first sequence, which is passed to the applet as

What is strange is that there is a helix where there are no 3bknmodA residues (e.g., in the N-terminal gap).
The secondary structure assignment is specified in an annotations file with the 3bknmodA sequence provided as the reference:

JALVIEW_ANNOTATION
SEQUENCE_REF 3bknmodA
BAR_GRAPH Score 0.06| 3.33| 1.68|-3.97|-1.44| 5.15| 0.97|-3.17|-3.01| 6.67|-3.19| 0.22| 5.66|-2.99|-3.08|-1.60|-4.00|-1.35| 4.88| 9.29| 0.86| 6.61|-1.60|-2.18| 0.11|-1.57|-1.47|-2.34|-3.20|-2.28| 0.09|-1.60|-1.56| 5.89|-1.59|-2.96|-3.17| 1.69| 2.06|-3.85| 0.03| 6.65|-1.44|-3.19| 9.99|-1.51|-3.94|-0.64| 3.32| 3.31|-0.65| 2.48| 1.83| 0.85| 0.00|-2.13|-4.00|-1.59| 0.86|-4.00| 0.91| 1.06|-2.37|-0.70| 5.19|-3.97|-0.77| 0.86|-2.31| 0.03|-3.96|-3.98| 0.01| 8.89| 6.64|-0.76| 1.61|-3.17| 0.17|-1.51|-3.96|-4.00|-2.40|-3.56| 6.82| 0.14|-1.56| 5.34| 0.94|-0.58|-3.01| 8.57|-1.53| 4.76|-0.64|-2.53|-1.47|-2.39|-1.50|-2.27| 0.22|-3.11|-2.37| 8.56|-1.51| 0.18|-3.10| 2.97| 2.12|-1.59| 1.55|-3.10|-1.57| 2.37|-3.20| 0.27| 7.74| 6.53|-0.77|-1.42| 9.90|-3.19|-3.98|-0.80|-4.00| 0.01| 1.75|-2.18|-4.79| 0.27|-1.50| 8.03| 7.46| 2.78|-3.20|-1.56| 8.82|-2.40| 0.00|-0.80|-0.80|0|0|0|0|0|0|0|0|0|0|
NO_GRAPH Secondary Structure H|H|H|H|H|H|H|H|H|H|H|H|H|H|H|H|H|H|H|H|H|H|H|H|H|H|H|||H|H|H|H|H|||||H|H|H|H|H|H|H|H|H|H|H|H|H|H|H|H|H|||||||||||||||||||H|H|H|H|H|H|H|H|H|H|H|H|H|H|H|H|H|H|H|H|H|H|H|H|H|H|H|H|H|||H|H|H|H|H|H|H|H|H|H|H|H|H|H|H|H|H|H|H|H|H|H|H|H|H|H|H|H|H|H|H||H|H|H|H|H|H|H|H||||||||

I thought I had all of this secondary structure stuff sorted out, but obviously not. Can someone tell me what I am doing wrong?

Best wishes,

Daron

2

Hello Daron.

Daron Standley wrote:

I thought I had all of this secondary structure stuff sorted out, but
obviously not. Can someone tell me what I am doing wrong?

It looks like a bug to me. The score annotation is correctly associated
with the sequence, but the secondary structure annotation is not (you
can see this when you edit the alignment, or when you output the
annotation to a text box). I'll have a look at the
jalview.io.AnnotationFile parser and see what its up to.

You can work around this by adding another SEQUENCE_REF entry before the
secondary structure row :

JALVIEW_ANNOTATION
SEQUENCE_REF 3bknmodA
BAR_GRAPH Score 0.06| 3.33| 1.68|-3.97|-1.44| 5.15| 0.97|-3.17|-3.01|
6.67|-3.19| 0.22| 5.66|-2.99|-3.08|-1.60|-4.00|-1.35| 4.88| 9.29| 0.86|
6.61|-1.60|-2.18| 0.11|-1.57|-1.47|-2.34|-3.20|-2.28| 0.09|-1.60|-1.56|
5.89|-1.59|-2.96|-3.17| 1.69| 2.06|-3.85| 0.03| 6.65|-1.44|-3.19|
9.99|-1.51|-3.94|-0.64| 3.32| 3.31|-0.65| 2.48| 1.83| 0.85|
0.00|-2.13|-4.00|-1.59| 0.86|-4.00| 0.91| 1.06|-2.37|-0.70|
5.19|-3.97|-0.77| 0.86|-2.31| 0.03|-3.96|-3.98| 0.01| 8.89| 6.64|-0.76|
1.61|-3.17| 0.17|-1.51|-3.96|-4.00|-2.40|-3.56| 6.82| 0.14|-1.56| 5.34|
0.94|-0.58|-3.01| 8.57|-1.53| 4.76|-0.64|-2.53|-1.47|-2.39|-1.50|-2.27|
0.22|-3.11|-2.37| 8.56|-1.51| 0.18|-3.10| 2.97| 2.12|-1.59|
1.55|-3.10|-1.57| 2.37|-3.20| 0.27| 7.74| 6.53|-0.77|-1.42|
9.90|-3.19|-3.98|-0.80|-4.00| 0.01| 1.75|-2.18|-4.79| 0.27|-1.50| 8.03|
7.46| 2.78|-3.20|-1.56| 8.82|-2.40| 0.00|-0.80|-0.80|0|0|0|0|0|0|0|0|0|0|
SEQUENCE_REF 3bknmodA
NO_GRAPH Secondary Structure
H>H>H>H>H>H>H>H>H>H>H>H>H>H>H>H>H>H>H>H>H>H>H>H>H>H>H>>>H>H>H>H>H>>>>>H>H>H>H>H>H>H>H>H>H>H>H>H>H>H>H>H>>>>>>>>>>>>>>>>>>>H>H>H>H>H>H>H>H>H>H>H>H>H>H>H>H>H>H>H>H>H>H>H>H>H>H>H>H>H>>>H>H>H>H>H>H>H>H>H>H>H>H>H>H>H>H>H>H>H>H>H>H>H>H>H>H>H>H>H>H>H>>H>H>H>H>H>H>H>H>>>>>>>>

perseverence always wins out in the end !
Jim

ยทยทยท

--
-------------------------------------------------------------------
J. B. Procter (ENFIN/VAMSAS) 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.