Hi everyone,
I really like Jalview. It could show hydrophobicity of my aligned amino acid sequences.
The number of aligned sequences is large. It will help to have average hydrophobicity at every position
For all the aligned seuqnces.
How can color scheme be converted to hydrophobicity score ?
Jalview colors every aa based on its hydrophobicity.
Can I access the numbers behind colors ?
I have attached one of my result.
Please help.
Best,
Rohit
Sent from Mail for Windows 10
Hello Rohit,
I’ve attached a groovy script that can be run to produce average hydrophobicity score annotation (copying in the list now we know it works for you!).
Tools | Groovy console | paste in the script and Script | Run.
I recommend choosing Jalview option Annotations | Autocalculated annotation | Show Last, so the new annotation stays above the others.
To answer your follow-up questions:
You can extract the annotation score values as CSV by right-click on the label at the left, option Export Annotation.
This works for all rows including the new Hydrophobicity scores.
You can copy the consensus sequence to the clipboard by right-click on ‘Consensus’ and ‘Copy Consensus Sequence’.
See http://www.jalview.org/help/html/menus/alwannotationpanel.html.
You can increase the font size of your alignment from the Jalview Format | Font menu.
Let us know if you have any more questions, and happy Jalviewing!
Kind regards,
Mungo
The University of Dundee is a registered Scottish Charity, No: SC015096
hydrophobicityScores.groovy (2.87 KB)
Mungo Carstairs
Jalview Computational Scientist
The Barton Group
Division of Computational Biology
School of Life Sciences
University of Dundee, Dundee, Scotland, UK
www.compbio.dundee.ac.uk
g.m.carstairs@dundee.ac.uk
We’re Scottish University of the Year again!
The Times / Sunday Times Good University Guide 2016 and 2017
From: jalview-discuss-bounces@jalview.org jalview-discuss-bounces@jalview.org on behalf of Dr. Rohit Jain rohit.mpibpc@gmail.com
Sent: 22 March 2019 02:15:48
To: jalview-discuss@jalview.org
Subject: [Jalview-discuss] How to plot hydrophobicity in multiple sequence alignment
Hi everyone,
I really like Jalview. It could show hydrophobicity of my aligned amino acid sequences.
The number of aligned sequences is large. It will help to have average hydrophobicity at every position
For all the aligned seuqnces.
How can color scheme be converted to hydrophobicity score ?
Jalview colors every aa based on its hydrophobicity.
Can I access the numbers behind colors ?
I have attached one of my result.
Please help.
Best,
Rohit
Sent from Mail for Windows 10
And just to add that, should you wish to, you can now use option ‘Select | Select/Hide Columns by Annotation’ to select (or hide!) columns above or below a threshold value for average hydrophobicity score.
Mungo
Mungo Carstairs
Jalview Computational Scientist
The Barton Group
Division of Computational Biology
School of Life Sciences
University of Dundee, Dundee, Scotland, UK
www.compbio.dundee.ac.uk
g.m.carstairs@dundee.ac.uk
We’re Scottish University of the Year again!
The Times / Sunday Times Good University Guide 2016 and 2017
From: jalview-discuss-bounces@jalview.org jalview-discuss-bounces@jalview.org on behalf of Mungo Carstairs (Staff) g.m.carstairs@dundee.ac.uk
Sent: 22 March 2019 13:41:02
To: Dr. Rohit Jain; jalview-discuss@jalview.org
Subject: Re: [Jalview-discuss] How to plot hydrophobicity in multiple sequence alignment
Hello Rohit,
I’ve attached a groovy script that can be run to produce average hydrophobicity score annotation (copying in the list now we know it works for you!).
Tools | Groovy console | paste in the script and Script | Run.
I recommend choosing Jalview option Annotations | Autocalculated annotation | Show Last, so the new annotation stays above the others.
To answer your follow-up questions:
You can extract the annotation score values as CSV by right-click on the label at the left, option Export Annotation.
This works for all rows including the new Hydrophobicity scores.
You can copy the consensus sequence to the clipboard by right-click on ‘Consensus’ and ‘Copy Consensus Sequence’.
See http://www.jalview.org/help/html/menus/alwannotationpanel.html.
You can increase the font size of your alignment from the Jalview Format | Font menu.
Let us know if you have any more questions, and happy Jalviewing!
Kind regards,
Mungo
Mungo Carstairs
Jalview Computational Scientist
The Barton Group
Division of Computational Biology
School of Life Sciences
University of Dundee, Dundee, Scotland, UK
www.compbio.dundee.ac.uk
g.m.carstairs@dundee.ac.uk
We’re Scottish University of the Year again!
The Times / Sunday Times Good University Guide 2016 and 2017
From: jalview-discuss-bounces@jalview.org jalview-discuss-bounces@jalview.org on behalf of Dr. Rohit Jain rohit.mpibpc@gmail.com
Sent: 22 March 2019 02:15:48
To: jalview-discuss@jalview.org
Subject: [Jalview-discuss] How to plot hydrophobicity in multiple sequence alignment
Hi everyone,
I really like Jalview. It could show hydrophobicity of my aligned amino acid sequences.
The number of aligned sequences is large. It will help to have average hydrophobicity at every position
For all the aligned seuqnces.
How can color scheme be converted to hydrophobicity score ?
Jalview colors every aa based on its hydrophobicity.
Can I access the numbers behind colors ?
I have attached one of my result.
Please help.
Best,
Rohit
Sent from Mail for Windows 10
The University of Dundee is a registered Scottish Charity, No: SC015096
The University of Dundee is a registered Scottish Charity, No: SC015096