It would be really helpful if the start and end coordinates of the matching sequences could be displayed in the ‘calculate pairwise alignment’ results.
…d
Dr David M A Martin PhD FRSB
Senior Lecturer in Bioinformatics
School of Life Sciences, University of Dundee
+44(0)1382 388704 | d.m.a.martin@dundee.ac.uk
We’re Scottish University of the Year again!
The Times / Sunday Times Good University Guide 2016 and 2017
Had a quick look at this.
The output is on screen and also in the console.
Looks like it could be doable with a combination of
report seq.getDisplayId(true) instead of seq.getName()
use SelectionGroup.getSelectionAsNewSequences() instead of SelectionGroup.getSequencesInOrder()
Current sequence ids get truncated to 30 characters in the report, which might be a bit severe with the range suffix added.
Mungo
The University of Dundee is a registered Scottish Charity, No: SC015096
ATT00001.txt (174 Bytes)
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 David Martin (Staff) d.m.a.martin@dundee.ac.uk
Sent: 23 August 2017 11:28
To: jalview-discuss@jalview.org
Subject: [Jalview-discuss] Piarwise alignment coordinates
It would be really helpful if the start and end coordinates of the matching sequences could be displayed in the ‘calculate pairwise alignment’ results.
…d
Dr David M A Martin PhD FRSB
Senior Lecturer in Bioinformatics
School of Life Sciences, University of Dundee
+44(0)1382 388704 | d.m.a.martin@dundee.ac.uk
We’re Scottish University of the Year again!
The Times / Sunday Times Good University Guide 2016 and 2017
The University of Dundee is a registered Scottish Charity, No: SC015096
This looks a lot like JAL-207 which is closed as Fixed in 2.8.2, but I am not convinced.
If you do a pairwise alignment of a sub-selection of two sequences and then view the result as an alignment, then start/end ranges are wrong and sequence features are wrongly located.
Suggest we re-open JAL-207?
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-dev-bounces@jalview.org jalview-dev-bounces@jalview.org on behalf of Mungo Carstairs (Staff) g.m.carstairs@dundee.ac.uk
Sent: 23 August 2017 12:19:16
To: Jalview Development List
Subject: [Jalview-dev] Fw: Pairwise alignment coordinates
Had a quick look at this.
The output is on screen and also in the console.
Looks like it could be doable with a combination of
report seq.getDisplayId(true) instead of seq.getName()
use SelectionGroup.getSelectionAsNewSequences() instead of SelectionGroup.getSequencesInOrder()
Current sequence ids get truncated to 30 characters in the report, which might be a bit severe with the range suffix added.
Mungo
The University of Dundee is a registered Scottish Charity, No: SC015096
The University of Dundee is a registered Scottish Charity, No: SC015096
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 David Martin (Staff) d.m.a.martin@dundee.ac.uk
Sent: 23 August 2017 11:28
To: jalview-discuss@jalview.org
Subject: [Jalview-discuss] Piarwise alignment coordinates
It would be really helpful if the start and end coordinates of the matching sequences could be displayed in the ‘calculate pairwise alignment’ results.
…d
Dr David M A Martin PhD FRSB
Senior Lecturer in Bioinformatics
School of Life Sciences, University of Dundee
+44(0)1382 388704 | d.m.a.martin@dundee.ac.uk
We’re Scottish University of the Year again!
The Times / Sunday Times Good University Guide 2016 and 2017
The University of Dundee is a registered Scottish Charity, No: SC015096
This looks a lot like JAL-207 which is closed as Fixed in 2.8.2, but I am not convinced.
slightly different scope - strictly speaking, JAL-207 is fixed, but wasn’t expanded to do what was needed.
If you do a pairwise alignment of a sub-selection of two sequences and then view the result as an alignment, then start/end ranges are wrong and sequence features are wrongly located.
yes.
Suggest we re-open JAL-207?
Opened as JAL-2684 and David’s original request as JAL-2685.
jim.
The University of Dundee is a registered Scottish Charity, No: SC015096
On 23/08/2017 14:03, Mungo Carstairs (Staff) wrote:
Hi
It would be really helpful if the start and end coordinates of the matching sequences could be displayed in the ‘calculate pairwise alignment’ results.
how did we miss that 
We’ll try and squeeze it in to the bug-fix release:
https://issues.jalview.org/browse/JAL-2685
jim
On 23/08/2017 11:28, David Martin (Staff) wrote:
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Dr JB Procter, Jalview Coordinator, The Barton Group
Division of Computational Biology, School of Life Sciences
University of Dundee, Dundee DD1 5EH, UK.
+44 1382 388734 | [www.jalview.org](http://www.jalview.org) | [www.compbio.dundee.ac.uk](http://www.compbio.dundee.ac.uk)