Representation of alignment as dots with reference sequence

Dear all,

I was wondering if there is an option in Jalview to representation alignment with a reference sequence (first row) and other sequences with dots for identity to this reference sequence?

Such as here: https://www.researchgate.net/figure/225287367_fig1_Multiple-sequence-alignment-of-target-primer-and-probe-sequences.-Dots-indicated

Thanks for your help,
Romain

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Romain Studer
EMBL-EBI
Wellcome Genome Campus
Hinxton
Cambridgeshire
CB10 1SD, UK
Tel: +44 (0)1223 492 547
Twitter: @RomainStuder

Hello Romain,

I think the menu option 'Format | Show nonconserved' may do what you want.

By default this will use the first sequence as the reference sequence.
You can also right-click on any sequence id and select
   <sequenceId> | Set as Reference
to select a different sequence as your reference sequence.

Best 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.jalview.org
www.compbio.dundee.ac.uk

···

________________________________________
From: jalview-discuss-bounces@jalview.org <jalview-discuss-bounces@jalview.org> on behalf of Romain Studer <rstuder@ebi.ac.uk>
Sent: 14 December 2015 11:08
To: Jalview-discuss@jalview.org
Subject: [Jalview-discuss] Representation of alignment as dots with reference sequence

Dear all,

I was wondering if there is an option in Jalview to representation
alignment with a reference sequence (first row) and other sequences with
dots for identity to this reference sequence?

Such as here:
https://www.researchgate.net/figure/225287367_fig1_Multiple-sequence-alignment-of-target-primer-and-probe-sequences.-Dots-indicated

Thanks for your help,
Romain

--
Romain Studer
EMBL-EBI
Wellcome Genome Campus
Hinxton
Cambridgeshire
CB10 1SD, UK
Tel: +44 (0)1223 492 547
Twitter: @RomainStuder

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Just a point of clarification .. what Mungo said isn't quite right:

By default this will use the first sequence as the reference sequence.

The 'Show nonconserved' option highlights differences to the currently
defined reference sequence, or the consensus for each column when no
reference is defined.

Hope that helps!
Jim.
ps. You can define a reference sequence for each group on the alignment,
useful when working with multiple sets of closely related sequences.

···

On 14/12/2015 11:24, Mungo Carstairs (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 | www.compbio.dundee.ac.uk