Hi all,
I am using Jalview now for DNA alignments and calculate consensus sequences, but noticed that when have “N” and “T” in the same column the consensus will give an “N”, while with any other nucleotide works as expected.
Is there any way to fix or edit how the DNA consensus is calculated?
Cheers,
jc
Hello Juan Carlos,
Before jumping in with a response, could you maybe just clarify, perhaps with a small example, what it is that you would expect to see that differs from what Jalview shows in the consensus?
Jalview is just treating N as another symbol for consensus purposes here. I wouldn’t expect N/T to behave any differently to N/G, N/C etc.
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.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 Juan Carlos Sanchez juancarlos.sanchez@adelaide.edu.au
Sent: 05 April 2017 06:59:43
To: jalview-discuss@jalview.org
Subject: [Jalview-discuss] DNA consensus
Hi all,
I am using Jalview now for DNA alignments and calculate consensus sequences, but noticed that when have “N” and “T” in the same column the consensus will give an “N”, while with any other nucleotide works as expected.
Is there any way to fix or edit how the DNA consensus is calculated?
Cheers,
jc
The University of Dundee is a registered Scottish Charity, No: SC015096
Hi Mungo,
Yes maybe an example is better.
A simple case with two sequences:
AAATATCCAGACGTAGGNNNNNNN
NNNNNNNCAGACGTAGGTTACCAT
Will give a consensus like
AAANANCCAGACGTAGGNNACCAN
Hope now is more clear.
Thanks!
jc
From: Mungo Carstairs (Staff) [mailto:g.m.carstairs@dundee.ac.uk]
Sent: Wednesday, 5 April 2017 4:53 PM
To: Juan Carlos Sanchez juancarlos.sanchez@adelaide.edu.au; jalview-discuss@jalview.org
Subject: Re: DNA consensus
Hello Juan Carlos,
Before jumping in with a response, could you maybe just clarify, perhaps with a small example, what it is that you would expect to see that differs from what Jalview shows in the consensus?
Jalview is just treating N as another symbol for consensus purposes here. I wouldn’t expect N/T to behave any differently to N/G, N/C etc.
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.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 Juan Carlos Sanchez <juancarlos.sanchez@adelaide.edu.au>
Sent: 05 April 2017 06:59:43
To: jalview-discuss@jalview.org
Subject: [Jalview-discuss] DNA consensus
Hi all,
I am using Jalview now for DNA alignments and calculate consensus sequences, but noticed that when have “N” and “T” in the same column the consensus will give an “N”, while with any other nucleotide works as expected.
Is there any way to fix or edit how the DNA consensus is calculated?
Cheers,
jc
The University of Dundee is a registered Scottish Charity, No: SC015096
Thanks JC,
If I view your example in Jalview, the consensus line shows 50/50 for
A/N, A/N, A/N, N/T, A/N, N/T, …
as I would expect.
Is it just the reordering of T/N (in the alignment) to N/T (in the consensus) that is giving the impression of an ‘N’ consensus in column 4?
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: Juan Carlos Sanchez juancarlos.sanchez@adelaide.edu.au
Sent: 05 April 2017 08:57:47
To: Mungo Carstairs (Staff); jalview-discuss@jalview.org
Subject: RE: DNA consensus
Hi Mungo,
Yes maybe an example is better.
A simple case with two sequences:
AAATATCCAGACGTAGGNNNNNNN
NNNNNNNCAGACGTAGGTTACCAT
Will give a consensus like
AAANANCCAGACGTAGGNNACCAN
Hope now is more clear.
Thanks!
jc
From: Mungo Carstairs (Staff) [mailto:g.m.carstairs@dundee.ac.uk]
Sent: Wednesday, 5 April 2017 4:53 PM
To: Juan Carlos Sanchez juancarlos.sanchez@adelaide.edu.au; jalview-discuss@jalview.org
Subject: Re: DNA consensus
Hello Juan Carlos,
Before jumping in with a response, could you maybe just clarify, perhaps with a small example, what it is that you would expect to see that differs from what Jalview shows in the consensus?
Jalview is just treating N as another symbol for consensus purposes here. I wouldn’t expect N/T to behave any differently to N/G, N/C etc.
Best regards,
Mungo
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 Juan Carlos Sanchez <juancarlos.sanchez@adelaide.edu.au>
Sent: 05 April 2017 06:59:43
To: jalview-discuss@jalview.org
Subject: [Jalview-discuss] DNA consensus
Hi all,
I am using Jalview now for DNA alignments and calculate consensus sequences, but noticed that when have “N” and “T” in the same column the consensus will give an “N”, while with any other nucleotide works as expected.
Is there any way to fix or edit how the DNA consensus is calculated?
Cheers,
jc
The University of Dundee is a registered Scottish Charity, No: SC015096