How to change numbering on my alignment?

kimsk · 31 August 2020 03:06

Hello,

I have an alignment of five sequences. Position 1 starts on one of the sequences, but I would like to change it to start on a different sequence. How can I do this?

Thank you,
Kate

g_m_carstairs · 31 August 2020 08:24

Hello Kate,

I’m not quite sure what the question is, so I’ll answer two ways.

You can change the order of sequences in the alignment by clicking on the sequence name and dragging them up or down.

You can change the start position of a sequence by right-clicking on the name, and following the popup menu to
| Edit Name/Description
and then type the desired /start-end after the sequence name, for example
myproteinname/20-88
If you don’t want to do the math(s) to work out the end position, just type /20-20 and Jalview will work it out for you.

Position numbering is per sequence, so changing it to “start on a different sequence” doesn’t make sense, or perhaps I haven’t understood your question properly.

···

One more detail: if you want to save your alignment as a Fasta (or other format) text file, then check/tick the box for “Append /start-end” for the file format in Jalview Preferences’ Output options panel. You’ll find Preferences under the Tools menu. If you don’t do this, sequences will revert to starting at position 1 after saving and reloading.

I hope that helps, if not please ask again!

Best,

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
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 Kate Kim kimsk@msg.ucsf.edu
Sent: 31 August 2020 04:06
To: jalview-discuss@jalview.org jalview-discuss@jalview.org
Subject: [Jalview-discuss] How to change numbering on my alignment?

Hello,

I have an alignment of five sequences. Position 1 starts on one of the sequences, but I would like to change it to start on a different sequence. How can I do this?

Thank you,
Kate

The University of Dundee is a registered Scottish Charity, No: SC015096

j_procter · 31 August 2020 09:59

Hello Kate.

Apologies for adding yet another response to Mungo's two suggestions.

Your email suggests the 'Position 1' you talk about is position '1' of the alignemnt ruler, which counts columns rather than sequence positions. If one of your sequences is longer than the others, and there are no insertions in the other sequences, then the ruler will indeed reflect the position of that sequence, but Jalview isn't doing anything special here - just showing the column numbers.

If you'd like to have the ruler show positions with respect to a particular sequence, however, then right-click on that sequence's ID and select the 'Set As Reference' option from the submenu. Now, the alignment ruler reflects positions with respect to your 'reference' sequence.

As Mungo says - if we still haven't worked out what you were asking, then let us know - but please also let us know if this helped you out !

Jim.

···

On 31/08/2020 09:24, Mungo Carstairs (Staff) wrote:

Hello Kate,

I'm not quite sure what the question is, so I'll answer two ways.

You can change the order of sequences in the alignment by clicking on the sequence name and dragging them up or down.

You can change the start position of a sequence by right-clicking on the name, and following the popup menu to
<Sequence Name> | Edit Name/Description
and then type the desired /start-end after the sequence name, for example
myproteinname/20-88
If you don't want to do the math(s) to work out the end position, just type /20-20 and Jalview will work it out for you.

Position numbering is per sequence, so changing it to "start on a different sequence" doesn't make sense, or perhaps I haven't understood your question properly.

One more detail: if you want to save your alignment as a Fasta (or other format) text file, then check/tick the box for "Append /start-end" for the file format in Jalview Preferences' Output options panel. You'll find Preferences under the Tools menu. If you don't do this, sequences will revert to starting at position 1 after saving and reloading.

I hope that helps, if not please ask again!

Best,

MungoEmail signature
University of Dundee shield logo <http://uod.ac.uk/sig-home>

*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 <http://www.jalview.org>

www.compbio.dundee.ac.uk <http://www.compbio.dundee.ac.uk>
g.m.carstairs@dundee.ac.uk <mailto:g.m.carstairs@dundee.ac.uk>

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*We're Scottish University of the Year again!* <http://uod.ac.uk/sig-strapline>
The Times / Sunday Times Good University Guide 2016 and 2017

------------------------------------------------------------------------
*From:* jalview-discuss-bounces@jalview.org <jalview-discuss-bounces@jalview.org> on behalf of Kate Kim <kimsk@msg.ucsf.edu>
*Sent:* 31 August 2020 04:06
*To:* jalview-discuss@jalview.org <jalview-discuss@jalview.org>
*Subject:* [Jalview-discuss] How to change numbering on my alignment?
Hello,

I have an alignment of five sequences. Position 1 starts on one of the sequences, but I would like to change it to start on a different sequence. How can I do this?

Thank you,
Kate

The University of Dundee is a registered Scottish Charity, No: SC015096

_______________________________________________
Jalview-discuss mailing list
Jalview-discuss@jalview.org
http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-discuss

--
-------------------------------------------------------------------
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

kimsk · 31 August 2020 20:17

Thank you Mungo and Jim! I apologize for not being very clear in my question. Thankfully, Jim’s last paragraph in the email was exactly what I needed, and my problem is solved

Thank you,
Kate

···

On Mon, Aug 31, 2020 at 2:59 AM James Procter <j.procter@dundee.ac.uk> wrote:

Hello Kate.

Apologies for adding yet another response to Mungo’s two suggestions.

Your email suggests the ‘Position 1’ you talk about is position ‘1’ of
the alignemnt ruler, which counts columns rather than sequence
positions. If one of your sequences is longer than the others, and there
are no insertions in the other sequences, then the ruler will indeed
reflect the position of that sequence, but Jalview isn’t doing anything
special here - just showing the column numbers.

If you’d like to have the ruler show positions with respect to a
particular sequence, however, then right-click on that sequence’s ID and
select the ‘Set As Reference’ option from the submenu. Now, the
alignment ruler reflects positions with respect to your ‘reference’
sequence.

As Mungo says - if we still haven’t worked out what you were asking,
then let us know - but please also let us know if this helped you out !

Jim.

On 31/08/2020 09:24, Mungo Carstairs (Staff) wrote:

Hello Kate,

I’m not quite sure what the question is, so I’ll answer two ways.

You can change the order of sequences in the alignment by clicking on
the sequence name and dragging them up or down.

You can change the start position of a sequence by right-clicking on the
name, and following the popup menu to
| Edit Name/Description
and then type the desired /start-end after the sequence name, for example
myproteinname/20-88
If you don’t want to do the math(s) to work out the end position, just
type /20-20 and Jalview will work it out for you.

Position numbering is per sequence, so changing it to “start on a
different sequence” doesn’t make sense, or perhaps I haven’t understood
your question properly.

One more detail: if you want to save your alignment as a Fasta (or other
format) text file, then check/tick the box for “Append /start-end” for
the file format in Jalview Preferences’ Output options panel. You’ll
find Preferences under the Tools menu. If you don’t do this, sequences
will revert to starting at position 1 after saving and reloading.

I hope that helps, if not please ask again!

Best,

MungoEmail signature
University of Dundee shield logo <http://uod.ac.uk/sig-home>

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 <http://www.jalview.org>

www.compbio.dundee.ac.uk <http://www.compbio.dundee.ac.uk>
g.m.carstairs@dundee.ac.uk mailto:[g.m.carstairs@dundee.ac.uk](mailto:g.m.carstairs@dundee.ac.uk)

University of Dundee Facebook <http://uod.ac.uk/sig-fb> University of
Dundee Twitter <http://uod.ac.uk/sig-tw> University of Dundee LinkedIn
<http://uod.ac.uk/sig-li> University of Dundee YouTube
<http://uod.ac.uk/sig-yt> University of Dundee Instagram
<http://uod.ac.uk/sig-ig> University of Dundee Snapchat
<http://uod.ac.uk/sig-sc>
We’re Scottish University of the Year again!
<http://uod.ac.uk/sig-strapline>
The Times / Sunday Times Good University Guide 2016 and 2017

From: jalview-discuss-bounces@jalview.org
<jalview-discuss-bounces@jalview.org> on behalf of Kate Kim
<kimsk@msg.ucsf.edu>
Sent: 31 August 2020 04:06
To: jalview-discuss@jalview.org <jalview-discuss@jalview.org>
Subject: [Jalview-discuss] How to change numbering on my alignment?
Hello,

I have an alignment of five sequences. Position 1 starts on one of the
sequences, but I would like to change it to start on a different
sequence. How can I do this?

Thank you,
Kate

The University of Dundee is a registered Scottish Charity, No: SC015096

Jalview-discuss mailing list
Jalview-discuss@jalview.org
http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-discuss

–

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